List of protein subcellular localization prediction tools (English Wikipedia)

Analysis of information sources in references of the Wikipedia article "List of protein subcellular localization prediction tools" in English language version.

refsWebsite

Global rank English rank

198nih.gov

4^th place

123doi.org

2^nd place

13semanticscholar.org

11^th place

8^th place

9worldcat.org

5^th place

4harvard.edu

18^th place

17^th place

3handle.net

102^nd place

76^th place

2psu.edu

207^th place

136^th place

1vital-it.ch

low place

doi.org

Tantoso E, Li KB (August 2008). "AAIndexLoc: predicting subcellular localization of proteins based on a new representation of sequences using amino acid indices". Amino Acids. 35 (2): 345–53. doi:10.1007/s00726-007-0616-y. PMID 18163182. S2CID 712299.
Saravanan V, Lakshmi PT (December 2013). "APSLAP: an adaptive boosting technique for predicting subcellular localization of apoptosis protein". Acta Biotheoretica. 61 (4): 481–97. doi:10.1007/s10441-013-9197-1. PMID 23982307. S2CID 23858443.
Kaundal R, Saini R, Zhao PX (September 2010). "Combining machine learning and homology-based approaches to accurately predict subcellular localization in Arabidopsis". Plant Physiology. 154 (1): 36–54. doi:10.1104/pp.110.156851. PMC 2938157. PMID 20647376.
Pierleoni A, Martelli PL, Fariselli P, Casadio R (July 2006). "BaCelLo: a balanced subcellular localization predictor". Bioinformatics. 22 (14): e408–16. doi:10.1093/bioinformatics/btl222. PMID 16873501.
Piovesan D, Martelli PL, Fariselli P, Zauli A, Rossi I, Casadio R (July 2011). "BAR-PLUS: the Bologna Annotation Resource Plus for functional and structural annotation of protein sequences". Nucleic Acids Research. 39 (Web Server issue): W197–202. doi:10.1093/nar/gkr292. PMC 3125743. PMID 21622657.
Profiti G, Martelli PL, Casadio R (July 2017). "The Bologna Annotation Resource (BAR 3.0): improving protein functional annotation". Nucleic Acids Research. 45 (W1): W285 – W290. doi:10.1093/nar/gkx330. PMC 5570247. PMID 28453653.
Van Domselaar GH, Stothard P, Shrivastava S, Cruz JA, Guo A, Dong X, Lu P, Szafron D, Greiner R, Wishart DS (July 2005). "BASys: a web server for automated bacterial genome annotation". Nucleic Acids Research. 33 (Web Server issue): W455–9. doi:10.1093/nar/gki593. PMC 1160269. PMID 15980511.
Berven FS, Flikka K, Jensen HB, Eidhammer I (July 2004). "BOMP: a program to predict integral beta-barrel outer membrane proteins encoded within genomes of Gram-negative bacteria". Nucleic Acids Research. 32 (Web Server issue): W394–9. doi:10.1093/nar/gkh351. PMC 441489. PMID 15215418.
Taylor PD, Attwood TK, Flower DR (July 2003). "BPROMPT: A consensus server for membrane protein prediction". Nucleic Acids Research. 31 (13): 3698–700. doi:10.1093/nar/gkg554. PMC 168961. PMID 12824397.
Savojard C, Martelli PL, Fariselli P, Profiti G, Casadio R (July 2018). "BUSCA: an integrative web server to predict subcellular localization of proteins". Nucleic Acids Research. 46 (W1): W459 – W466. doi:10.1093/nar/gky320. PMC 6031068. PMID 29718411.
Chou KC, Shen HB (2008-01-01). "Cell-PLoc: a package of Web servers for predicting subcellular localization of proteins in various organisms". Nature Protocols. 3 (2): 153–62. doi:10.1038/nprot.2007.494. PMID 18274516. S2CID 226104.
Yu CS, Lin CJ, Hwang JK (May 2004). "Predicting subcellular localization of proteins for Gram-negative bacteria by support vector machines based on n-peptide compositions". Protein Science. 13 (5): 1402–6. doi:10.1110/ps.03479604. PMC 2286765. PMID 15096640.
Yu CS, Chen YC, Lu CH, Hwang JK (August 2006). "Prediction of protein subcellular localization". Proteins. 64 (3): 643–51. doi:10.1002/prot.21018. PMID 16752418. S2CID 24245346.
Paramasivam N, Linke D (2011). "ClubSub-P: Cluster-Based Subcellular Localization Prediction for Gram-Negative Bacteria and Archaea". Frontiers in Microbiology. 2: 218. doi:10.3389/fmicb.2011.00218. PMC 3210502. PMID 22073040.
Goudenège D, Avner S, Lucchetti-Miganeh C, Barloy-Hubler F (March 2010). "CoBaltDB: Complete bacterial and archaeal orfeomes subcellular localization database and associated resources". BMC Microbiology. 10: 88. doi:10.1186/1471-2180-10-88. PMC 2850352. PMID 20331850.
Coronnello C, Benos PV (July 2013). "ComiR: Combinatorial microRNA target prediction tool". Nucleic Acids Research. 41 (Web Server issue): W159–64. doi:10.1093/nar/gkt379. PMC 3692082. PMID 23703208.
Hooper CM, Castleden IR, Aryamanesh N, Jacoby RP, Millar AH (January 2016). "Finding the Subcellular Location of Barley, Wheat, Rice and Maize Proteins: The Compendium of Crop Proteins with Annotated Locations (cropPAL)". Plant & Cell Physiology. 57 (1): e9. doi:10.1093/pcp/pcv170. PMID 26556651.
Cserzö, Miklos; Eisenhaber, Frank; Eisenhaber, Birgit; Simon, Istvan (Sep 2002). "On filtering false positive transmembrane protein predictions". Protein Engineering, Design and Selection. 15 (9): 745–752. doi:10.1093/protein/15.9.745. ISSN 1741-0134. PMID 12456873.
Almagro Armenteros JJ, Sønderby CK, Sønderby SK, Nielsen H, Winther O (November 2017). "DeepLoc: prediction of protein subcellular localization using deep learning". Bioinformatics. 33 (21): 3387–3395. doi:10.1093/bioinformatics/btx431. PMID 29036616.
Stärk H, Dallago C, Heinzinger M, Rost B (November 2021). "Light Attention Predicts Protein Location from the Language of Life". Bioinformatics Advances. 1 (1): vbab035. doi:10.1093/bioadv/vbab035. PMC 9710637. PMID 36700108.
Maragkakis M, Reczko M, Simossis VA, Alexiou P, Papadopoulos GL, Dalamagas T, Giannopoulos G, Goumas G, Koukis E, Kourtis K, Vergoulis T, Koziris N, Sellis T, Tsanakas P, Hatzigeorgiou AG (July 2009). "DIANA-microT web server: elucidating microRNA functions through target prediction". Nucleic Acids Research. 37 (Web Server issue): W273–6. doi:10.1093/nar/gkp292. PMC 2703977. PMID 19406924.
Paraskevopoulou MD, Georgakilas G, Kostoulas N, Vlachos IS, Vergoulis T, Reczko M, Filippidis C, Dalamagas T, Hatzigeorgiou AG (July 2013). "DIANA-microT web server v5.0: service integration into miRNA functional analysis workflows". Nucleic Acids Research. 41 (Web Server issue): W169–73. doi:10.1093/nar/gkt393. PMC 3692048. PMID 23680784.
Wishart DS, Knox C, Guo AC, Shrivastava S, Hassanali M, Stothard P, Chang Z, Woolsey J (January 2006). "DrugBank: a comprehensive resource for in silico drug discovery and exploration". Nucleic Acids Research. 34 (Database issue): D668–72. doi:10.1093/nar/gkj067. PMC 1347430. PMID 16381955.
Horler RS, Butcher A, Papangelopoulos N, Ashton PD, Thomas GH (January 2009). "EchoLOCATION: an in silico analysis of the subcellular locations of Escherichia coli proteins and comparison with experimentally derived locations". Bioinformatics. 25 (2): 163–6. doi:10.1093/bioinformatics/btn596. PMID 19015139.
Fucile G, Di Biase D, Nahal H, La G, Khodabandeh S, Chen Y, Easley K, Christendat D, Kelley L, Provart NJ (January 2011). "ePlant and the 3D data display initiative: integrative systems biology on the world wide web". PLOS ONE. 6 (1): e15237. Bibcode:2011PLoSO...615237F. doi:10.1371/journal.pone.0015237. PMC 3018417. PMID 21249219.
Bhasin M, Raghava GP (July 2004). "ESLpred: SVM-based method for subcellular localization of eukaryotic proteins using dipeptide composition and PSI-BLAST". Nucleic Acids Research. 32 (Web Server issue): W414–9. doi:10.1093/nar/gkh350. PMC 441488. PMID 15215421.
Chou KC, Shen HB (April 2010). "A new method for predicting the subcellular localization of eukaryotic proteins with both single and multiple sites: Euk-mPLoc 2.0". PLOS ONE. 5 (4): e9931. Bibcode:2010PLoSO...5.9931C. doi:10.1371/journal.pone.0009931. PMC 2848569. PMID 20368981.
Ye H, Ye L, Kang H, Zhang D, Tao L, Tang K, Liu X, Zhu R, Liu Q, Chen YZ, Li Y, Cao Z (January 2011). "HIT: linking herbal active ingredients to targets". Nucleic Acids Research. 39 (Database issue): D1055–9. doi:10.1093/nar/gkq1165. PMC 3013727. PMID 21097881.
Tusnády, Gábor E.; Simon, István (Oct 1998). "Principles governing amino acid composition of integral membrane proteins: application to topology prediction 1 1Edited by J. Thornton". Journal of Molecular Biology. 283 (2): 489–506. doi:10.1006/jmbi.1998.2107. ISSN 0022-2836. PMID 9769220.
Tusnady, G. E.; Simon, I. (2001-09-01). "The HMMTOP transmembrane topology prediction server". Bioinformatics. 17 (9): 849–850. doi:10.1093/bioinformatics/17.9.849. ISSN 1367-4803. PMID 11590105.
Garg A, Bhasin M, Raghava GP (April 2005). "Support vector machine-based method for subcellular localization of human proteins using amino acid compositions, their order, and similarity search". The Journal of Biological Chemistry. 280 (15): 14427–32. doi:10.1074/jbc.M411789200. PMID 15647269.
Wang JC, Chu PY, Chen CM, Lin JH (July 2012). "idTarget: a web server for identifying protein targets of small chemical molecules with robust scoring functions and a divide-and-conquer docking approach". Nucleic Acids Research. 40 (Web Server issue): W393–9. doi:10.1093/nar/gks496. PMC 3394295. PMID 22649057.
Chou KC, Wu ZC, Xiao X (February 2012). "iLoc-Hum: using the accumulation-label scale to predict subcellular locations of human proteins with both single and multiple sites". Molecular BioSystems. 8 (2): 629–41. doi:10.1039/c1mb05420a. PMID 22134333.
Lin HN, Chen CT, Sung TY, Ho SY, Hsu WL (December 2009). "Protein subcellular localization prediction of eukaryotes using a knowledge-based approach". BMC Bioinformatics. 10 (Suppl 15): S8. doi:10.1186/1471-2105-10-S15-S8. PMC 2788359. PMID 19958518.
Amaral PP, Clark MB, Gascoigne DK, Dinger ME, Mattick JS (January 2011). "lncRNAdb: a reference database for long noncoding RNAs". Nucleic Acids Research. 39 (Database issue): D146–51. doi:10.1093/nar/gkq1138. PMC 3013714. PMID 21112873.
Nair R, Rost B (July 2003). "LOC3D: annotate sub-cellular localization for protein structures". Nucleic Acids Research. 31 (13): 3337–40. doi:10.1093/nar/gkg514. PMC 168921. PMID 12824321.
Nair R, Rost B (April 2005). "Mimicking cellular sorting improves prediction of subcellular localization". Journal of Molecular Biology. 348 (1): 85–100. doi:10.1016/j.jmb.2005.02.025. PMID 15808855.
Nair R, Rost B (December 2003). "Better prediction of sub-cellular localization by combining evolutionary and structural information". Proteins. 53 (4): 917–30. CiteSeerX 10.1.1.217.389. doi:10.1002/prot.10507. PMID 14635133. S2CID 3142627.
Fink JL, Aturaliya RN, Davis MJ, Zhang F, Hanson K, Teasdale MS, Kai C, Kawai J, Carninci P, Hayashizaki Y, Teasdale RD (January 2006). "LOCATE: a mouse protein subcellular localization database". Nucleic Acids Research. 34 (Database issue): D213–7. doi:10.1093/nar/gkj069. PMC 1347432. PMID 16381849.
Rastogi S, Rost B (January 2011). "LocDB: experimental annotations of localization for Homo sapiens and Arabidopsis thaliana". Nucleic Acids Research. 39 (Database issue): D230–4. doi:10.1093/nar/gkq927. PMC 3013784. PMID 21071420.
Nair R, Rost B (July 2004). "LOCnet and LOCtarget: sub-cellular localization for structural genomics targets". Nucleic Acids Research. 32 (Web Server issue): W517–21. doi:10.1093/nar/gkh441. PMC 441579. PMID 15215440.
Goldberg T, Hamp T, Rost B (September 2012). "LocTree2 predicts localization for all domains of life". Bioinformatics. 28 (18): i458 – i465. doi:10.1093/bioinformatics/bts390. PMC 3436817. PMID 22962467.
Goldberg T, Hecht M, Hamp T, Karl T, Yachdav G, Ahmed N, Altermann U, Angerer P, Ansorge S, Balasz K, Bernhofer M, Betz A, Cizmadija L, Do KT, Gerke J, Greil R, Joerdens V, Hastreiter M, Hembach K, Herzog M, Kalemanov M, Kluge M, Meier A, Nasir H, Neumaier U, Prade V, Reeb J, Sorokoumov A, Troshani I, Vorberg S, Waldraff S, Zierer J, Nielsen H, Rost B (July 2014). "LocTree3 prediction of localization". Nucleic Acids Research. 42 (Web Server issue): W350–5. doi:10.1093/nar/gku396. PMC 4086075. PMID 24848019.
Panwar B, Raghava GP (May 2012). "Predicting sub-cellular localization of tRNA synthetases from their primary structures". Amino Acids. 42 (5): 1703–13. doi:10.1007/s00726-011-0872-8. PMID 21400228. S2CID 2996097.
Simha R, Briesemeister S, Kohlbacher O, Shatkay H (June 2015). "Protein (multi-)location prediction: utilizing interdependencies via a generative model". Bioinformatics. 31 (12): i365–74. doi:10.1093/bioinformatics/btv264. PMC 4765880. PMID 26072505.
Pierleoni A, Martelli PL, Casadio R (May 2011). "MemLoci: predicting subcellular localization of membrane proteins in eukaryotes". Bioinformatics. 27 (9): 1224–30. doi:10.1093/bioinformatics/btr108. PMID 21367869.
Pierleoni A, Indio V, Savojardo C, Fariselli P, Martelli PL, Casadio R (July 2011). "MemPype: a pipeline for the annotation of eukaryotic membrane proteins". Nucleic Acids Research. 39 (Web Server issue): W375–80. doi:10.1093/nar/gkr282. PMC 3125734. PMID 21543452.
Magnus M, Pawlowski M, Bujnicki JM (December 2012). "MetaLocGramN: A meta-predictor of protein subcellular localization for Gram-negative bacteria". Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics. 1824 (12): 1425–33. doi:10.1016/j.bbapap.2012.05.018. PMID 22705560.
Hausser J, Berninger P, Rodak C, Jantscher Y, Wirth S, Zavolan M (July 2009). "MirZ: an integrated microRNA expression atlas and target prediction resource". Nucleic Acids Research. 37 (Web Server issue): W266–72. doi:10.1093/nar/gkp412. PMC 2703880. PMID 19468042.
Kumar M, Verma R, Raghava GP (March 2006). "Prediction of mitochondrial proteins using support vector machine and hidden Markov model". The Journal of Biological Chemistry. 281 (9): 5357–63. doi:10.1074/jbc.M511061200. PMID 16339140.
Höglund A, Dönnes P, Blum T, Adolph HW, Kohlbacher O (May 2006). "MultiLoc: prediction of protein subcellular localization using N-terminal targeting sequences, sequence motifs and amino acid composition". Bioinformatics. 22 (10): 1158–65. doi:10.1093/bioinformatics/btl002. PMID 16428265.
Zhu PP, Li WC, Zhong ZJ, Deng EZ, Ding H, Chen W, Lin H (February 2015). "Predicting the subcellular localization of mycobacterial proteins by incorporating the optimal tripeptides into the general form of pseudo amino acid composition". Molecular BioSystems. 11 (2): 558–63. doi:10.1039/c4mb00645c. PMID 25437899. S2CID 8130819.
la Cour T, Kiemer L, Mølgaard A, Gupta R, Skriver K, Brunak S (June 2004). "Analysis and prediction of leucine-rich nuclear export signals". Protein Engineering, Design & Selection. 17 (6): 527–36. doi:10.1093/protein/gzh062. PMID 15314210.
King, Brian R; Guda, Chittibabu (2007). "ngLOC: an n-gram-based Bayesian method for estimating the subcellular proteomes of eukaryotes". Genome Biology. 8 (5): R68. doi:10.1186/gb-2007-8-5-r68. ISSN 1465-6906. PMC 1929137. PMID 17472741.
Woodcroft BJ, Hammond L, Stow JL, Hamilton NA (November 2009). "Automated organelle-based colocalization in whole-cell imaging". Cytometry. Part A. 75 (11): 941–50. doi:10.1002/cyto.a.20786. PMID 19746416. S2CID 25068671.
Lu Z, Szafron D, Greiner R, Lu P, Wishart DS, Poulin B, Anvik J, Macdonell C, Eisner R (March 2004). "Predicting subcellular localization of proteins using machine-learned classifiers". Bioinformatics. 20 (4): 547–56. CiteSeerX 10.1.1.216.1493. doi:10.1093/bioinformatics/btg447. PMID 14990451.
Szafron D, Lu P, Greiner R, Wishart DS, Poulin B, Eisner R, Lu Z, Anvik J, Macdonell C, Fyshe A, Meeuwis D (July 2004). "Proteome Analyst: custom predictions with explanations in a web-based tool for high-throughput proteome annotations". Nucleic Acids Research. 32 (Web Server issue): W365–71. doi:10.1093/nar/gkh485. PMC 441623. PMID 15215412.
Liu X, Ouyang S, Yu B, Liu Y, Huang K, Gong J, Zheng S, Li Z, Li H, Jiang H (July 2010). "PharmMapper server: a web server for potential drug target identification using pharmacophore mapping approach". Nucleic Acids Research. 38 (Web Server issue): W609–14. doi:10.1093/nar/gkq300. PMC 2896160. PMID 20430828.
Tang S, Li T, Cong P, Xiong W, Wang Z, Sun J (July 2013). "PlantLoc: an accurate web server for predicting plant protein subcellular localization by substantiality motif". Nucleic Acids Research. 41 (Web Server issue): W441–7. doi:10.1093/nar/gkt428. PMC 3692052. PMID 23729470.
Bagos PG, Liakopoulos TD, Spyropoulos IC, Hamodrakas SJ (July 2004). "PRED-TMBB: a web server for predicting the topology of beta-barrel outer membrane proteins". Nucleic Acids Research. 32 (Web Server issue): W400–4. doi:10.1093/nar/gkh417. PMC 441555. PMID 15215419.
Bagos PG, Liakopoulos TD, Spyropoulos IC, Hamodrakas SJ (March 2004). "A Hidden Markov Model method, capable of predicting and discriminating beta-barrel outer membrane proteins". BMC Bioinformatics. 5: 29. doi:10.1186/1471-2105-5-29. PMC 385222. PMID 15070403.
Cokol M, Nair R, Rost B (November 2000). "Finding nuclear localization signals". EMBO Reports. 1 (5): 411–5. doi:10.1093/embo-reports/kvd092. PMC 1083765. PMID 11258480.
Yachdav G, Kloppmann E, Kajan L, Hecht M, Goldberg T, Hamp T, Hönigschmid P, Schafferhans A, Roos M, Bernhofer M, Richter L, Ashkenazy H, Punta M, Schlessinger A, Bromberg Y, Schneider R, Vriend G, Sander C, Ben-Tal N, Rost B (July 2014). "PredictProtein--an open resource for online prediction of protein structural and functional features". Nucleic Acids Research. 42 (Web Server issue): W337–43. doi:10.1093/nar/gku366. PMC 4086098. PMID 24799431.
Kaján L, Yachdav G, Vicedo E, Steinegger M, Mirdita M, Angermüller C, Böhm A, Domke S, Ertl J, Mertes C, Reisinger E, Staniewski C, Rost B (2013). "Cloud prediction of protein structure and function with PredictProtein for Debian". BioMed Research International. 2013: 1–6. doi:10.1155/2013/398968. PMC 3732596. PMID 23971032.
Rost B, Liu J (July 2003). "The PredictProtein server". Nucleic Acids Research. 31 (13): 3300–4. doi:10.1093/nar/gkg508. PMC 168915. PMID 12824312.
Rost B, Yachdav G, Liu J (July 2004). "The PredictProtein server". Nucleic Acids Research. 32 (Web Server issue): W321–6. doi:10.1093/nar/gkh377. PMC 441515. PMID 15215403.
Mower JP (July 2009). "The PREP suite: predictive RNA editors for plant mitochondrial genes, chloroplast genes and user-defined alignments". Nucleic Acids Research. 37 (Web Server issue): W253–9. doi:10.1093/nar/gkp337. PMC 2703948. PMID 19433507.
Mower JP (April 2005). "PREP-Mt: predictive RNA editor for plant mitochondrial genes". BMC Bioinformatics. 6: 96. doi:10.1186/1471-2105-6-96. PMC 1087475. PMID 15826309.
Huang WL, Tung CW, Ho SW, Hwang SF, Ho SY (February 2008). "ProLoc-GO: utilizing informative Gene Ontology terms for sequence-based prediction of protein subcellular localization". BMC Bioinformatics. 9: 80. doi:10.1186/1471-2105-9-80. PMC 2262056. PMID 18241343.
Huang WL, Tung CW, Huang HL, Hwang SF, Ho SY (2007). "ProLoc: prediction of protein subnuclear localization using SVM with automatic selection from physicochemical composition features". Bio Systems. 90 (2): 573–81. doi:10.1016/j.biosystems.2007.01.001. PMID 17291684.
Yang B, Sayers S, Xiang Z, He Y (January 2011). "Protegen: a web-based protective antigen database and analysis system". Nucleic Acids Research. 39 (Database issue): D1073–8. doi:10.1093/nar/gkq944. PMC 3013795. PMID 20959289.
Drwal, Malgorzata N.; Banerjee, Priyanka; Dunkel, Mathias; Wettig, Martin R.; Preissner, Robert (2014-05-16). "ProTox: a web server for the in silico prediction of rodent oral toxicity". Nucleic Acids Research. 42 (W1): W53 – W58. doi:10.1093/nar/gku401. ISSN 1362-4962. PMC 4086068. PMID 24838562.
Banerjee, Priyanka; Eckert, Andreas O; Schrey, Anna K; Preissner, Robert (2018-04-30). "ProTox-II: a webserver for the prediction of toxicity of chemicals". Nucleic Acids Research. 46 (W1): W257 – W263. doi:10.1093/nar/gky318. ISSN 0305-1048. PMC 6031011. PMID 29718510.
Bhasin M, Garg A, Raghava GP (May 2005). "PSLpred: prediction of subcellular localization of bacterial proteins". Bioinformatics. 21 (10): 2522–4. doi:10.1093/bioinformatics/bti309. PMID 15699023.
Yu NY, Wagner JR, Laird MR, Melli G, Rey S, Lo R, Dao P, Sahinalp SC, Ester M, Foster LJ, Brinkman FS (July 2010). "PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes". Bioinformatics. 26 (13): 1608–15. doi:10.1093/bioinformatics/btq249. PMC 2887053. PMID 20472543.
Yu NY, Laird MR, Spencer C, Brinkman FS (January 2011). "PSORTdb--an expanded, auto-updated, user-friendly protein subcellular localization database for Bacteria and Archaea". Nucleic Acids Research. 39 (Database issue): D241–4. doi:10.1093/nar/gkq1093. PMC 3013690. PMID 21071402.
Rey S, Acab M, Gardy JL, Laird MR, deFays K, Lambert C, Brinkman FS (January 2005). "PSORTdb: a protein subcellular localization database for bacteria". Nucleic Acids Research. 33 (Database issue): D164–8. doi:10.1093/nar/gki027. PMC 539981. PMID 15608169.
Wu HJ, Ma YK, Chen T, Wang M, Wang XJ (July 2012). "PsRobot: a web-based plant small RNA meta-analysis toolbox". Nucleic Acids Research. 40 (Web Server issue): W22–8. doi:10.1093/nar/gks554. PMC 3394341. PMID 22693224.
Guda C, Subramaniam S (November 2005). "pTARGET [corrected] a new method for predicting protein subcellular localization in eukaryotes". Bioinformatics. 21 (21): 3963–9. doi:10.1093/bioinformatics/bti650. PMID 16144808.
Guda C (July 2006). "pTARGET: a web server for predicting protein subcellular localization". Nucleic Acids Research. 34 (Web Server issue): W210–3. doi:10.1093/nar/gkl093. PMC 1538910. PMID 16844995.
Xinyi Z, Yitong T, Yunhao B, Fei C, Caroline U (July 2024). "Prediction of protein subcellular localization in single cells". bioRxiv. doi:10.1101/2024.07.25.605178. PMC 11291118.
Lee TY, Bo-Kai Hsu J, Chang WC, Huang HD (January 2011). "RegPhos: a system to explore the protein kinase-substrate phosphorylation network in humans". Nucleic Acids Research. 39 (Database issue): D777–87. doi:10.1093/nar/gkq970. PMC 3013804. PMID 21037261.
Elefant N, Berger A, Shein H, Hofree M, Margalit H, Altuvia Y (January 2011). "RepTar: a database of predicted cellular targets of host and viral miRNAs". Nucleic Acids Research. 39 (Database issue): D188–94. doi:10.1093/nar/gkq1233. PMC 3013742. PMID 21149264.
Eggenhofer F, Tafer H, Stadler PF, Hofacker IL (July 2011). "RNApredator: fast accessibility-based prediction of sRNA targets". Nucleic Acids Research. 39 (Web Server issue): W149–54. doi:10.1093/nar/gkr467. PMC 3125805. PMID 21672960.
Shao W, Liu M, Zhang D (January 2016). "Human cell structure-driven model construction for predicting protein subcellular location from biological images". Bioinformatics. 32 (1): 114–21. doi:10.1093/bioinformatics/btv521. PMID 26363175.
Savojardo C, Martelli PL, Fariselli P, Casadio R (February 2017). "SChloro: directing Viridiplantae proteins to six chloroplastic sub-compartments". Bioinformatics. 33 (3): 347–353. doi:10.1093/bioinformatics/btw656. PMC 5408801. PMID 28172591.
Saravanan V, Lakshmi PT (February 2013). "SCLAP: an adaptive boosting method for predicting subchloroplast localization of plant proteins". OMICS. 17 (2): 106–15. doi:10.1089/omi.2012.0070. PMID 23289782.
Mooney C, Wang YH, Pollastri G (October 2011). "SCLpred: protein subcellular localization prediction by N-to-1 neural networks". Bioinformatics. 27 (20): 2812–9. doi:10.1093/bioinformatics/btr494. hdl:10197/3443. PMID 21873639.
Kaleel, M; Zheng, Y; Chen, J; Feng, X; Simpson, JC; Pollastri, G; Mooney, C (6 March 2020). "SCLpred-EMS: subcellular localization prediction of endomembrane system and secretory pathway proteins by Deep N-to-1 Convolutional Neural Networks". Bioinformatics. 36 (11): 3343–3349. doi:10.1093/bioinformatics/btaa156. hdl:10197/12182. PMID 32142105.
Kaleel, Manaz; Ellinger, Liam; Lalor, Clodagh; Pollastri, Gianluca; Mooney, Catherine (2021). "SCLpred-MEM: Subcellular localization prediction of membrane proteins by deep N-to-1 convolutional neural networks". Proteins: Structure, Function, and Bioinformatics. 89 (10): 1233–1239. doi:10.1002/prot.26144. hdl:2346/90320. PMID 33983651. S2CID 234484678.
Bendtsen JD, Jensen LJ, Blom N, Von Heijne G, Brunak S (April 2004). "Feature-based prediction of non-classical and leaderless protein secretion". Protein Engineering, Design & Selection. 17 (4): 349–56. doi:10.1093/protein/gzh037. PMID 15115854.
Bendtsen JD, Kiemer L, Fausbøll A, Brunak S (October 2005). "Non-classical protein secretion in bacteria". BMC Microbiology. 5: 58. doi:10.1186/1471-2180-5-58. PMC 1266369. PMID 16212653.
Xu YY, Yang F, Zhang Y, Shen HB (April 2015). "Bioimaging-based detection of mislocalized proteins in human cancers by semi-supervised learning". Bioinformatics. 31 (7): 1111–9. doi:10.1093/bioinformatics/btu772. PMC 4382902. PMID 25414362.
Shatkay H, Höglund A, Brady S, Blum T, Dönnes P, Kohlbacher O (June 2007). "SherLoc: high-accuracy prediction of protein subcellular localization by integrating text and protein sequence data". Bioinformatics. 23 (11): 1410–7. doi:10.1093/bioinformatics/btm115. PMID 17392328.
Tanz SK, Castleden I, Hooper CM, Vacher M, Small I, Millar HA (January 2013). "SUBA3: a database for integrating experimentation and prediction to define the SUBcellular location of proteins in Arabidopsis". Nucleic Acids Research. 41 (Database issue): D1185–91. doi:10.1093/nar/gks1151. PMC 3531127. PMID 23180787.
Hooper CM, Tanz SK, Castleden IR, Vacher MA, Small ID, Millar AH (December 2014). "SUBAcon: a consensus algorithm for unifying the subcellular localization data of the Arabidopsis proteome". Bioinformatics. 30 (23): 3356–64. doi:10.1093/bioinformatics/btu550. PMID 25150248.
Du P, Cao S, Li Y (November 2009). "SubChlo: predicting protein subchloroplast locations with pseudo-amino acid composition and the evidence-theoretic K-nearest neighbor (ET-KNN) algorithm". Journal of Theoretical Biology. 261 (2): 330–5. Bibcode:2009JThBi.261..330D. doi:10.1016/j.jtbi.2009.08.004. PMID 19679138.
Dunkel M, Günther S, Ahmed J, Wittig B, Preissner R (July 2008). "SuperPred: drug classification and target prediction". Nucleic Acids Research. 36 (Web Server issue): W55–9. doi:10.1093/nar/gkn307. PMC 2447784. PMID 18499712.
Hecker N, Ahmed J, von Eichborn J, Dunkel M, Macha K, Eckert A, Gilson MK, Bourne PE, Preissner R (January 2012). "SuperTarget goes quantitative: update on drug-target interactions". Nucleic Acids Research. 40 (Database issue): D1113–7. doi:10.1093/nar/gkr912. PMC 3245174. PMID 22067455.
Gfeller, David; Michielin, Olivier; Zoete, Vincent (2013-09-17). "Shaping the interaction landscape of bioactive molecules". Bioinformatics. 29 (23): 3073–3079. doi:10.1093/bioinformatics/btt540. ISSN 1460-2059. PMID 24048355.
Gfeller, David; Grosdidier, Aurélien; Wirth, Matthias; Daina, Antoine; Michielin, Olivier; Zoete, Vincent (2014-05-03). "SwissTargetPrediction: a web server for target prediction of bioactive small molecules". Nucleic Acids Research. 42 (W1): W32 – W38. doi:10.1093/nar/gku293. ISSN 1362-4962. PMC 4086140. PMID 24792161.
Lim E, Pon A, Djoumbou Y, Knox C, Shrivastava S, Guo AC, Neveu V, Wishart DS (January 2010). "T3DB: a comprehensively annotated database of common toxins and their targets". Nucleic Acids Research. 38 (Database issue): D781–6. doi:10.1093/nar/gkp934. PMC 2808899. PMID 19897546.
Doyle EL, Booher NJ, Standage DS, Voytas DF, Brendel VP, Vandyk JK, Bogdanove AJ (July 2012). "TAL Effector-Nucleotide Targeter (TALE-NT) 2.0: tools for TAL effector design and target prediction". Nucleic Acids Research. 40 (Web Server issue): W117–22. doi:10.1093/nar/gks608. PMC 3394250. PMID 22693217.
Li H, Gao Z, Kang L, Zhang H, Yang K, Yu K, Luo X, Zhu W, Chen K, Shen J, Wang X, Jiang H (July 2006). "TarFisDock: a web server for identifying drug targets with docking approach". Nucleic Acids Research. 34 (Web Server issue): W219–24. doi:10.1093/nar/gkl114. PMC 1538869. PMID 16844997.
Tjaden B (July 2008). "TargetRNA: a tool for predicting targets of small RNA action in bacteria". Nucleic Acids Research. 36 (Web Server issue): W109–13. doi:10.1093/nar/gkn264. PMC 2447797. PMID 18477632.
Emanuelsson O, Nielsen H, Brunak S, Von Heijne G (July 2000). "Predicting subcellular localization of proteins based on their N-terminal amino acid sequence". Journal of Molecular Biology. 300 (4): 1005–16. doi:10.1006/jmbi.2000.3903. PMID 10891285.
Magariños MP, Carmona SJ, Crowther GJ, Ralph SA, Roos DS, Shanmugam D, Van Voorhis WC, Agüero F (January 2012). "TDR Targets: a chemogenomics resource for neglected diseases". Nucleic Acids Research. 40 (Database issue): D1118–27. doi:10.1093/nar/gkr1053. PMC 3245062. PMID 22116064.
Lin H, Chen W, Yuan LF, Li ZQ, Ding H (June 2013). "Using over-represented tetrapeptides to predict protein submitochondria locations". Acta Biotheoretica. 61 (2): 259–68. doi:10.1007/s10441-013-9181-9. PMID 23475502. S2CID 30809970.
Gromiha MM, Ahmad S, Suwa M (April 2004). "Neural network-based prediction of transmembrane beta-strand segments in outer membrane proteins". Journal of Computational Chemistry. 25 (5): 762–7. doi:10.1002/jcc.10386. PMID 14978719. S2CID 3486330.
Gromiha MM, Ahmad S, Suwa M (July 2005). "TMBETA-NET: discrimination and prediction of membrane spanning beta-strands in outer membrane proteins". Nucleic Acids Research. 33 (Web Server issue): W164–7. doi:10.1093/nar/gki367. PMC 1160128. PMID 15980447.
Krogh, Anders; Larsson, Björn; von Heijne, Gunnar; Sonnhammer, Erik L.L (Jan 2001). "Predicting transmembrane protein topology with a hidden markov model: application to complete genomes". Journal of Molecular Biology. 305 (3): 567–580. doi:10.1006/jmbi.2000.4315. ISSN 0022-2836. PMID 11152613.
Indio V, Martelli PL, Savojardo C, Fariselli P, Casadio R (April 2013). "The prediction of organelle-targeting peptides in eukaryotic proteins with Grammatical-Restrained Hidden Conditional Random Fields". Bioinformatics. 29 (8): 981–8. doi:10.1093/bioinformatics/btt089. PMID 23428638.
Savojardo C, Martelli PL, Fariselli P, Casadio R (October 2015). "TPpred3 detects and discriminates mitochondrial and chloroplastic targeting peptides in eukaryotic proteins". Bioinformatics. 31 (20): 3269–75. doi:10.1093/bioinformatics/btv367. PMID 26079349.
Zhu F, Han B, Kumar P, Liu X, Ma X, Wei X, Huang L, Guo Y, Han L, Zheng C, Chen Y (January 2010). "Update of TTD: Therapeutic Target Database". Nucleic Acids Research. 38 (Database issue): D787–91. doi:10.1093/nar/gkp1014. PMC 2808971. PMID 19933260.
Ellis LB, Gao J, Fenner K, Wackett LP (July 2008). "The University of Minnesota pathway prediction system: predicting metabolic logic". Nucleic Acids Research. 36 (Web Server issue): W427–32. doi:10.1093/nar/gkn315. PMC 2447765. PMID 18524801.
Horton P, Park KJ, Obayashi T, Fujita N, Harada H, Adams-Collier CJ, Nakai K (July 2007). "WoLF PSORT: protein localization predictor". Nucleic Acids Research. 35 (Web Server issue): W585–7. doi:10.1093/nar/gkm259. PMC 1933216. PMID 17517783.
Briesemeister S, Rahnenführer J, Kohlbacher O (July 2010). "YLoc--an interpretable web server for predicting subcellular localization". Nucleic Acids Research. 38 (Web Server issue): W497–502. doi:10.1093/nar/gkq477. PMC 2896088. PMID 20507917.
Blancafort P, Magnenat L, Barbas CF (March 2003). "Scanning the human genome with combinatorial transcription factor libraries". Nature Biotechnology. 21 (3): 269–74. doi:10.1038/nbt794. PMID 12592412. S2CID 9761535.
Dreier B, Fuller RP, Segal DJ, Lund CV, Blancafort P, Huber A, Koksch B, Barbas CF (October 2005). "Development of zinc finger domains for recognition of the 5'-CNN-3' family DNA sequences and their use in the construction of artificial transcription factors". The Journal of Biological Chemistry. 280 (42): 35588–97. doi:10.1074/jbc.M506654200. PMID 16107335.
Dreier B, Segal DJ, Barbas CF (November 2000). "Insights into the molecular recognition of the 5'-GNN-3' family of DNA sequences by zinc finger domains". Journal of Molecular Biology. 303 (4): 489–502. doi:10.1006/jmbi.2000.4133. PMID 11054286. S2CID 11263372.
Mandell JG, Barbas CF (July 2006). "Zinc Finger Tools: custom DNA-binding domains for transcription factors and nucleases". Nucleic Acids Research. 34 (Web Server issue): W516–23. doi:10.1093/nar/gkl209. PMC 1538883. PMID 16845061.
Dreier B, Beerli RR, Segal DJ, Flippin JD, Barbas CF (August 2001). "Development of zinc finger domains for recognition of the 5'-ANN-3' family of DNA sequences and their use in the construction of artificial transcription factors". The Journal of Biological Chemistry. 276 (31): 29466–78. doi:10.1074/jbc.M102604200. PMID 11340073.
Segal DJ, Dreier B, Beerli RR, Barbas CF (March 1999). "Toward controlling gene expression at will: selection and design of zinc finger domains recognizing each of the 5'-GNN-3' DNA target sequences". Proceedings of the National Academy of Sciences of the United States of America. 96 (6): 2758–63. Bibcode:1999PNAS...96.2758S. doi:10.1073/pnas.96.6.2758. PMC 15842. PMID 10077584.

handle.net

hdl.handle.net

Mooney C, Wang YH, Pollastri G (October 2011). "SCLpred: protein subcellular localization prediction by N-to-1 neural networks". Bioinformatics. 27 (20): 2812–9. doi:10.1093/bioinformatics/btr494. hdl:10197/3443. PMID 21873639.
Kaleel, M; Zheng, Y; Chen, J; Feng, X; Simpson, JC; Pollastri, G; Mooney, C (6 March 2020). "SCLpred-EMS: subcellular localization prediction of endomembrane system and secretory pathway proteins by Deep N-to-1 Convolutional Neural Networks". Bioinformatics. 36 (11): 3343–3349. doi:10.1093/bioinformatics/btaa156. hdl:10197/12182. PMID 32142105.
Kaleel, Manaz; Ellinger, Liam; Lalor, Clodagh; Pollastri, Gianluca; Mooney, Catherine (2021). "SCLpred-MEM: Subcellular localization prediction of membrane proteins by deep N-to-1 convolutional neural networks". Proteins: Structure, Function, and Bioinformatics. 89 (10): 1233–1239. doi:10.1002/prot.26144. hdl:2346/90320. PMID 33983651. S2CID 234484678.

harvard.edu

ui.adsabs.harvard.edu

Fucile G, Di Biase D, Nahal H, La G, Khodabandeh S, Chen Y, Easley K, Christendat D, Kelley L, Provart NJ (January 2011). "ePlant and the 3D data display initiative: integrative systems biology on the world wide web". PLOS ONE. 6 (1): e15237. Bibcode:2011PLoSO...615237F. doi:10.1371/journal.pone.0015237. PMC 3018417. PMID 21249219.
Chou KC, Shen HB (April 2010). "A new method for predicting the subcellular localization of eukaryotic proteins with both single and multiple sites: Euk-mPLoc 2.0". PLOS ONE. 5 (4): e9931. Bibcode:2010PLoSO...5.9931C. doi:10.1371/journal.pone.0009931. PMC 2848569. PMID 20368981.
Du P, Cao S, Li Y (November 2009). "SubChlo: predicting protein subchloroplast locations with pseudo-amino acid composition and the evidence-theoretic K-nearest neighbor (ET-KNN) algorithm". Journal of Theoretical Biology. 261 (2): 330–5. Bibcode:2009JThBi.261..330D. doi:10.1016/j.jtbi.2009.08.004. PMID 19679138.
Segal DJ, Dreier B, Beerli RR, Barbas CF (March 1999). "Toward controlling gene expression at will: selection and design of zinc finger domains recognizing each of the 5'-GNN-3' DNA target sequences". Proceedings of the National Academy of Sciences of the United States of America. 96 (6): 2758–63. Bibcode:1999PNAS...96.2758S. doi:10.1073/pnas.96.6.2758. PMC 15842. PMID 10077584.

nih.gov

pubmed.ncbi.nlm.nih.gov

Tantoso E, Li KB (August 2008). "AAIndexLoc: predicting subcellular localization of proteins based on a new representation of sequences using amino acid indices". Amino Acids. 35 (2): 345–53. doi:10.1007/s00726-007-0616-y. PMID 18163182. S2CID 712299.
Saravanan V, Lakshmi PT (December 2013). "APSLAP: an adaptive boosting technique for predicting subcellular localization of apoptosis protein". Acta Biotheoretica. 61 (4): 481–97. doi:10.1007/s10441-013-9197-1. PMID 23982307. S2CID 23858443.
Kaundal R, Saini R, Zhao PX (September 2010). "Combining machine learning and homology-based approaches to accurately predict subcellular localization in Arabidopsis". Plant Physiology. 154 (1): 36–54. doi:10.1104/pp.110.156851. PMC 2938157. PMID 20647376.
Pierleoni A, Martelli PL, Fariselli P, Casadio R (July 2006). "BaCelLo: a balanced subcellular localization predictor". Bioinformatics. 22 (14): e408–16. doi:10.1093/bioinformatics/btl222. PMID 16873501.
Piovesan D, Martelli PL, Fariselli P, Zauli A, Rossi I, Casadio R (July 2011). "BAR-PLUS: the Bologna Annotation Resource Plus for functional and structural annotation of protein sequences". Nucleic Acids Research. 39 (Web Server issue): W197–202. doi:10.1093/nar/gkr292. PMC 3125743. PMID 21622657.
Profiti G, Martelli PL, Casadio R (July 2017). "The Bologna Annotation Resource (BAR 3.0): improving protein functional annotation". Nucleic Acids Research. 45 (W1): W285 – W290. doi:10.1093/nar/gkx330. PMC 5570247. PMID 28453653.
Van Domselaar GH, Stothard P, Shrivastava S, Cruz JA, Guo A, Dong X, Lu P, Szafron D, Greiner R, Wishart DS (July 2005). "BASys: a web server for automated bacterial genome annotation". Nucleic Acids Research. 33 (Web Server issue): W455–9. doi:10.1093/nar/gki593. PMC 1160269. PMID 15980511.
Berven FS, Flikka K, Jensen HB, Eidhammer I (July 2004). "BOMP: a program to predict integral beta-barrel outer membrane proteins encoded within genomes of Gram-negative bacteria". Nucleic Acids Research. 32 (Web Server issue): W394–9. doi:10.1093/nar/gkh351. PMC 441489. PMID 15215418.
Taylor PD, Attwood TK, Flower DR (July 2003). "BPROMPT: A consensus server for membrane protein prediction". Nucleic Acids Research. 31 (13): 3698–700. doi:10.1093/nar/gkg554. PMC 168961. PMID 12824397.
Savojard C, Martelli PL, Fariselli P, Profiti G, Casadio R (July 2018). "BUSCA: an integrative web server to predict subcellular localization of proteins". Nucleic Acids Research. 46 (W1): W459 – W466. doi:10.1093/nar/gky320. PMC 6031068. PMID 29718411.
Chou KC, Shen HB (2008-01-01). "Cell-PLoc: a package of Web servers for predicting subcellular localization of proteins in various organisms". Nature Protocols. 3 (2): 153–62. doi:10.1038/nprot.2007.494. PMID 18274516. S2CID 226104.
Yu CS, Lin CJ, Hwang JK (May 2004). "Predicting subcellular localization of proteins for Gram-negative bacteria by support vector machines based on n-peptide compositions". Protein Science. 13 (5): 1402–6. doi:10.1110/ps.03479604. PMC 2286765. PMID 15096640.
Yu CS, Chen YC, Lu CH, Hwang JK (August 2006). "Prediction of protein subcellular localization". Proteins. 64 (3): 643–51. doi:10.1002/prot.21018. PMID 16752418. S2CID 24245346.
Paramasivam N, Linke D (2011). "ClubSub-P: Cluster-Based Subcellular Localization Prediction for Gram-Negative Bacteria and Archaea". Frontiers in Microbiology. 2: 218. doi:10.3389/fmicb.2011.00218. PMC 3210502. PMID 22073040.
Goudenège D, Avner S, Lucchetti-Miganeh C, Barloy-Hubler F (March 2010). "CoBaltDB: Complete bacterial and archaeal orfeomes subcellular localization database and associated resources". BMC Microbiology. 10: 88. doi:10.1186/1471-2180-10-88. PMC 2850352. PMID 20331850.
Coronnello C, Benos PV (July 2013). "ComiR: Combinatorial microRNA target prediction tool". Nucleic Acids Research. 41 (Web Server issue): W159–64. doi:10.1093/nar/gkt379. PMC 3692082. PMID 23703208.
Hooper CM, Castleden IR, Aryamanesh N, Jacoby RP, Millar AH (January 2016). "Finding the Subcellular Location of Barley, Wheat, Rice and Maize Proteins: The Compendium of Crop Proteins with Annotated Locations (cropPAL)". Plant & Cell Physiology. 57 (1): e9. doi:10.1093/pcp/pcv170. PMID 26556651.
Cserzö, Miklos; Eisenhaber, Frank; Eisenhaber, Birgit; Simon, Istvan (Sep 2002). "On filtering false positive transmembrane protein predictions". Protein Engineering, Design and Selection. 15 (9): 745–752. doi:10.1093/protein/15.9.745. ISSN 1741-0134. PMID 12456873.
Almagro Armenteros JJ, Sønderby CK, Sønderby SK, Nielsen H, Winther O (November 2017). "DeepLoc: prediction of protein subcellular localization using deep learning". Bioinformatics. 33 (21): 3387–3395. doi:10.1093/bioinformatics/btx431. PMID 29036616.
Stärk H, Dallago C, Heinzinger M, Rost B (November 2021). "Light Attention Predicts Protein Location from the Language of Life". Bioinformatics Advances. 1 (1): vbab035. doi:10.1093/bioadv/vbab035. PMC 9710637. PMID 36700108.
Maragkakis M, Reczko M, Simossis VA, Alexiou P, Papadopoulos GL, Dalamagas T, Giannopoulos G, Goumas G, Koukis E, Kourtis K, Vergoulis T, Koziris N, Sellis T, Tsanakas P, Hatzigeorgiou AG (July 2009). "DIANA-microT web server: elucidating microRNA functions through target prediction". Nucleic Acids Research. 37 (Web Server issue): W273–6. doi:10.1093/nar/gkp292. PMC 2703977. PMID 19406924.
Paraskevopoulou MD, Georgakilas G, Kostoulas N, Vlachos IS, Vergoulis T, Reczko M, Filippidis C, Dalamagas T, Hatzigeorgiou AG (July 2013). "DIANA-microT web server v5.0: service integration into miRNA functional analysis workflows". Nucleic Acids Research. 41 (Web Server issue): W169–73. doi:10.1093/nar/gkt393. PMC 3692048. PMID 23680784.
Wishart DS, Knox C, Guo AC, Shrivastava S, Hassanali M, Stothard P, Chang Z, Woolsey J (January 2006). "DrugBank: a comprehensive resource for in silico drug discovery and exploration". Nucleic Acids Research. 34 (Database issue): D668–72. doi:10.1093/nar/gkj067. PMC 1347430. PMID 16381955.
Horler RS, Butcher A, Papangelopoulos N, Ashton PD, Thomas GH (January 2009). "EchoLOCATION: an in silico analysis of the subcellular locations of Escherichia coli proteins and comparison with experimentally derived locations". Bioinformatics. 25 (2): 163–6. doi:10.1093/bioinformatics/btn596. PMID 19015139.
Fucile G, Di Biase D, Nahal H, La G, Khodabandeh S, Chen Y, Easley K, Christendat D, Kelley L, Provart NJ (January 2011). "ePlant and the 3D data display initiative: integrative systems biology on the world wide web". PLOS ONE. 6 (1): e15237. Bibcode:2011PLoSO...615237F. doi:10.1371/journal.pone.0015237. PMC 3018417. PMID 21249219.
Bhasin M, Raghava GP (July 2004). "ESLpred: SVM-based method for subcellular localization of eukaryotic proteins using dipeptide composition and PSI-BLAST". Nucleic Acids Research. 32 (Web Server issue): W414–9. doi:10.1093/nar/gkh350. PMC 441488. PMID 15215421.
Chou KC, Shen HB (April 2010). "A new method for predicting the subcellular localization of eukaryotic proteins with both single and multiple sites: Euk-mPLoc 2.0". PLOS ONE. 5 (4): e9931. Bibcode:2010PLoSO...5.9931C. doi:10.1371/journal.pone.0009931. PMC 2848569. PMID 20368981.
Ye H, Ye L, Kang H, Zhang D, Tao L, Tang K, Liu X, Zhu R, Liu Q, Chen YZ, Li Y, Cao Z (January 2011). "HIT: linking herbal active ingredients to targets". Nucleic Acids Research. 39 (Database issue): D1055–9. doi:10.1093/nar/gkq1165. PMC 3013727. PMID 21097881.
Tusnády, Gábor E.; Simon, István (Oct 1998). "Principles governing amino acid composition of integral membrane proteins: application to topology prediction 1 1Edited by J. Thornton". Journal of Molecular Biology. 283 (2): 489–506. doi:10.1006/jmbi.1998.2107. ISSN 0022-2836. PMID 9769220.
Tusnady, G. E.; Simon, I. (2001-09-01). "The HMMTOP transmembrane topology prediction server". Bioinformatics. 17 (9): 849–850. doi:10.1093/bioinformatics/17.9.849. ISSN 1367-4803. PMID 11590105.
Garg A, Bhasin M, Raghava GP (April 2005). "Support vector machine-based method for subcellular localization of human proteins using amino acid compositions, their order, and similarity search". The Journal of Biological Chemistry. 280 (15): 14427–32. doi:10.1074/jbc.M411789200. PMID 15647269.
Wang JC, Chu PY, Chen CM, Lin JH (July 2012). "idTarget: a web server for identifying protein targets of small chemical molecules with robust scoring functions and a divide-and-conquer docking approach". Nucleic Acids Research. 40 (Web Server issue): W393–9. doi:10.1093/nar/gks496. PMC 3394295. PMID 22649057.
Chou KC, Wu ZC, Xiao X (February 2012). "iLoc-Hum: using the accumulation-label scale to predict subcellular locations of human proteins with both single and multiple sites". Molecular BioSystems. 8 (2): 629–41. doi:10.1039/c1mb05420a. PMID 22134333.
Lin HN, Chen CT, Sung TY, Ho SY, Hsu WL (December 2009). "Protein subcellular localization prediction of eukaryotes using a knowledge-based approach". BMC Bioinformatics. 10 (Suppl 15): S8. doi:10.1186/1471-2105-10-S15-S8. PMC 2788359. PMID 19958518.
Amaral PP, Clark MB, Gascoigne DK, Dinger ME, Mattick JS (January 2011). "lncRNAdb: a reference database for long noncoding RNAs". Nucleic Acids Research. 39 (Database issue): D146–51. doi:10.1093/nar/gkq1138. PMC 3013714. PMID 21112873.
Nair R, Rost B (July 2003). "LOC3D: annotate sub-cellular localization for protein structures". Nucleic Acids Research. 31 (13): 3337–40. doi:10.1093/nar/gkg514. PMC 168921. PMID 12824321.
Nair R, Rost B (April 2005). "Mimicking cellular sorting improves prediction of subcellular localization". Journal of Molecular Biology. 348 (1): 85–100. doi:10.1016/j.jmb.2005.02.025. PMID 15808855.
Nair R, Rost B (December 2003). "Better prediction of sub-cellular localization by combining evolutionary and structural information". Proteins. 53 (4): 917–30. CiteSeerX 10.1.1.217.389. doi:10.1002/prot.10507. PMID 14635133. S2CID 3142627.
Fink JL, Aturaliya RN, Davis MJ, Zhang F, Hanson K, Teasdale MS, Kai C, Kawai J, Carninci P, Hayashizaki Y, Teasdale RD (January 2006). "LOCATE: a mouse protein subcellular localization database". Nucleic Acids Research. 34 (Database issue): D213–7. doi:10.1093/nar/gkj069. PMC 1347432. PMID 16381849.
Rastogi S, Rost B (January 2011). "LocDB: experimental annotations of localization for Homo sapiens and Arabidopsis thaliana". Nucleic Acids Research. 39 (Database issue): D230–4. doi:10.1093/nar/gkq927. PMC 3013784. PMID 21071420.
Nair R, Rost B (July 2004). "LOCnet and LOCtarget: sub-cellular localization for structural genomics targets". Nucleic Acids Research. 32 (Web Server issue): W517–21. doi:10.1093/nar/gkh441. PMC 441579. PMID 15215440.
Goldberg T, Hamp T, Rost B (September 2012). "LocTree2 predicts localization for all domains of life". Bioinformatics. 28 (18): i458 – i465. doi:10.1093/bioinformatics/bts390. PMC 3436817. PMID 22962467.
Goldberg T, Hecht M, Hamp T, Karl T, Yachdav G, Ahmed N, Altermann U, Angerer P, Ansorge S, Balasz K, Bernhofer M, Betz A, Cizmadija L, Do KT, Gerke J, Greil R, Joerdens V, Hastreiter M, Hembach K, Herzog M, Kalemanov M, Kluge M, Meier A, Nasir H, Neumaier U, Prade V, Reeb J, Sorokoumov A, Troshani I, Vorberg S, Waldraff S, Zierer J, Nielsen H, Rost B (July 2014). "LocTree3 prediction of localization". Nucleic Acids Research. 42 (Web Server issue): W350–5. doi:10.1093/nar/gku396. PMC 4086075. PMID 24848019.
Panwar B, Raghava GP (May 2012). "Predicting sub-cellular localization of tRNA synthetases from their primary structures". Amino Acids. 42 (5): 1703–13. doi:10.1007/s00726-011-0872-8. PMID 21400228. S2CID 2996097.
Simha R, Briesemeister S, Kohlbacher O, Shatkay H (June 2015). "Protein (multi-)location prediction: utilizing interdependencies via a generative model". Bioinformatics. 31 (12): i365–74. doi:10.1093/bioinformatics/btv264. PMC 4765880. PMID 26072505.
Pierleoni A, Martelli PL, Casadio R (May 2011). "MemLoci: predicting subcellular localization of membrane proteins in eukaryotes". Bioinformatics. 27 (9): 1224–30. doi:10.1093/bioinformatics/btr108. PMID 21367869.
Pierleoni A, Indio V, Savojardo C, Fariselli P, Martelli PL, Casadio R (July 2011). "MemPype: a pipeline for the annotation of eukaryotic membrane proteins". Nucleic Acids Research. 39 (Web Server issue): W375–80. doi:10.1093/nar/gkr282. PMC 3125734. PMID 21543452.
Magnus M, Pawlowski M, Bujnicki JM (December 2012). "MetaLocGramN: A meta-predictor of protein subcellular localization for Gram-negative bacteria". Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics. 1824 (12): 1425–33. doi:10.1016/j.bbapap.2012.05.018. PMID 22705560.
Hausser J, Berninger P, Rodak C, Jantscher Y, Wirth S, Zavolan M (July 2009). "MirZ: an integrated microRNA expression atlas and target prediction resource". Nucleic Acids Research. 37 (Web Server issue): W266–72. doi:10.1093/nar/gkp412. PMC 2703880. PMID 19468042.
Kumar M, Verma R, Raghava GP (March 2006). "Prediction of mitochondrial proteins using support vector machine and hidden Markov model". The Journal of Biological Chemistry. 281 (9): 5357–63. doi:10.1074/jbc.M511061200. PMID 16339140.
Höglund A, Dönnes P, Blum T, Adolph HW, Kohlbacher O (May 2006). "MultiLoc: prediction of protein subcellular localization using N-terminal targeting sequences, sequence motifs and amino acid composition". Bioinformatics. 22 (10): 1158–65. doi:10.1093/bioinformatics/btl002. PMID 16428265.
Zhu PP, Li WC, Zhong ZJ, Deng EZ, Ding H, Chen W, Lin H (February 2015). "Predicting the subcellular localization of mycobacterial proteins by incorporating the optimal tripeptides into the general form of pseudo amino acid composition". Molecular BioSystems. 11 (2): 558–63. doi:10.1039/c4mb00645c. PMID 25437899. S2CID 8130819.
la Cour T, Kiemer L, Mølgaard A, Gupta R, Skriver K, Brunak S (June 2004). "Analysis and prediction of leucine-rich nuclear export signals". Protein Engineering, Design & Selection. 17 (6): 527–36. doi:10.1093/protein/gzh062. PMID 15314210.
King, Brian R; Guda, Chittibabu (2007). "ngLOC: an n-gram-based Bayesian method for estimating the subcellular proteomes of eukaryotes". Genome Biology. 8 (5): R68. doi:10.1186/gb-2007-8-5-r68. ISSN 1465-6906. PMC 1929137. PMID 17472741.
Woodcroft BJ, Hammond L, Stow JL, Hamilton NA (November 2009). "Automated organelle-based colocalization in whole-cell imaging". Cytometry. Part A. 75 (11): 941–50. doi:10.1002/cyto.a.20786. PMID 19746416. S2CID 25068671.
Lu Z, Szafron D, Greiner R, Lu P, Wishart DS, Poulin B, Anvik J, Macdonell C, Eisner R (March 2004). "Predicting subcellular localization of proteins using machine-learned classifiers". Bioinformatics. 20 (4): 547–56. CiteSeerX 10.1.1.216.1493. doi:10.1093/bioinformatics/btg447. PMID 14990451.
Szafron D, Lu P, Greiner R, Wishart DS, Poulin B, Eisner R, Lu Z, Anvik J, Macdonell C, Fyshe A, Meeuwis D (July 2004). "Proteome Analyst: custom predictions with explanations in a web-based tool for high-throughput proteome annotations". Nucleic Acids Research. 32 (Web Server issue): W365–71. doi:10.1093/nar/gkh485. PMC 441623. PMID 15215412.
Liu X, Ouyang S, Yu B, Liu Y, Huang K, Gong J, Zheng S, Li Z, Li H, Jiang H (July 2010). "PharmMapper server: a web server for potential drug target identification using pharmacophore mapping approach". Nucleic Acids Research. 38 (Web Server issue): W609–14. doi:10.1093/nar/gkq300. PMC 2896160. PMID 20430828.
Tang S, Li T, Cong P, Xiong W, Wang Z, Sun J (July 2013). "PlantLoc: an accurate web server for predicting plant protein subcellular localization by substantiality motif". Nucleic Acids Research. 41 (Web Server issue): W441–7. doi:10.1093/nar/gkt428. PMC 3692052. PMID 23729470.
Bagos PG, Liakopoulos TD, Spyropoulos IC, Hamodrakas SJ (July 2004). "PRED-TMBB: a web server for predicting the topology of beta-barrel outer membrane proteins". Nucleic Acids Research. 32 (Web Server issue): W400–4. doi:10.1093/nar/gkh417. PMC 441555. PMID 15215419.
Bagos PG, Liakopoulos TD, Spyropoulos IC, Hamodrakas SJ (March 2004). "A Hidden Markov Model method, capable of predicting and discriminating beta-barrel outer membrane proteins". BMC Bioinformatics. 5: 29. doi:10.1186/1471-2105-5-29. PMC 385222. PMID 15070403.
Cokol M, Nair R, Rost B (November 2000). "Finding nuclear localization signals". EMBO Reports. 1 (5): 411–5. doi:10.1093/embo-reports/kvd092. PMC 1083765. PMID 11258480.
Yachdav G, Kloppmann E, Kajan L, Hecht M, Goldberg T, Hamp T, Hönigschmid P, Schafferhans A, Roos M, Bernhofer M, Richter L, Ashkenazy H, Punta M, Schlessinger A, Bromberg Y, Schneider R, Vriend G, Sander C, Ben-Tal N, Rost B (July 2014). "PredictProtein--an open resource for online prediction of protein structural and functional features". Nucleic Acids Research. 42 (Web Server issue): W337–43. doi:10.1093/nar/gku366. PMC 4086098. PMID 24799431.
Kaján L, Yachdav G, Vicedo E, Steinegger M, Mirdita M, Angermüller C, Böhm A, Domke S, Ertl J, Mertes C, Reisinger E, Staniewski C, Rost B (2013). "Cloud prediction of protein structure and function with PredictProtein for Debian". BioMed Research International. 2013: 1–6. doi:10.1155/2013/398968. PMC 3732596. PMID 23971032.
Rost B, Liu J (July 2003). "The PredictProtein server". Nucleic Acids Research. 31 (13): 3300–4. doi:10.1093/nar/gkg508. PMC 168915. PMID 12824312.
Rost B, Yachdav G, Liu J (July 2004). "The PredictProtein server". Nucleic Acids Research. 32 (Web Server issue): W321–6. doi:10.1093/nar/gkh377. PMC 441515. PMID 15215403.
Mower JP (July 2009). "The PREP suite: predictive RNA editors for plant mitochondrial genes, chloroplast genes and user-defined alignments". Nucleic Acids Research. 37 (Web Server issue): W253–9. doi:10.1093/nar/gkp337. PMC 2703948. PMID 19433507.
Mower JP (April 2005). "PREP-Mt: predictive RNA editor for plant mitochondrial genes". BMC Bioinformatics. 6: 96. doi:10.1186/1471-2105-6-96. PMC 1087475. PMID 15826309.
Huang WL, Tung CW, Ho SW, Hwang SF, Ho SY (February 2008). "ProLoc-GO: utilizing informative Gene Ontology terms for sequence-based prediction of protein subcellular localization". BMC Bioinformatics. 9: 80. doi:10.1186/1471-2105-9-80. PMC 2262056. PMID 18241343.
Huang WL, Tung CW, Huang HL, Hwang SF, Ho SY (2007). "ProLoc: prediction of protein subnuclear localization using SVM with automatic selection from physicochemical composition features". Bio Systems. 90 (2): 573–81. doi:10.1016/j.biosystems.2007.01.001. PMID 17291684.
Yang B, Sayers S, Xiang Z, He Y (January 2011). "Protegen: a web-based protective antigen database and analysis system". Nucleic Acids Research. 39 (Database issue): D1073–8. doi:10.1093/nar/gkq944. PMC 3013795. PMID 20959289.
Drwal, Malgorzata N.; Banerjee, Priyanka; Dunkel, Mathias; Wettig, Martin R.; Preissner, Robert (2014-05-16). "ProTox: a web server for the in silico prediction of rodent oral toxicity". Nucleic Acids Research. 42 (W1): W53 – W58. doi:10.1093/nar/gku401. ISSN 1362-4962. PMC 4086068. PMID 24838562.
Banerjee, Priyanka; Eckert, Andreas O; Schrey, Anna K; Preissner, Robert (2018-04-30). "ProTox-II: a webserver for the prediction of toxicity of chemicals". Nucleic Acids Research. 46 (W1): W257 – W263. doi:10.1093/nar/gky318. ISSN 0305-1048. PMC 6031011. PMID 29718510.
Bhasin M, Garg A, Raghava GP (May 2005). "PSLpred: prediction of subcellular localization of bacterial proteins". Bioinformatics. 21 (10): 2522–4. doi:10.1093/bioinformatics/bti309. PMID 15699023.
Yu NY, Wagner JR, Laird MR, Melli G, Rey S, Lo R, Dao P, Sahinalp SC, Ester M, Foster LJ, Brinkman FS (July 2010). "PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes". Bioinformatics. 26 (13): 1608–15. doi:10.1093/bioinformatics/btq249. PMC 2887053. PMID 20472543.
Yu NY, Laird MR, Spencer C, Brinkman FS (January 2011). "PSORTdb--an expanded, auto-updated, user-friendly protein subcellular localization database for Bacteria and Archaea". Nucleic Acids Research. 39 (Database issue): D241–4. doi:10.1093/nar/gkq1093. PMC 3013690. PMID 21071402.
Rey S, Acab M, Gardy JL, Laird MR, deFays K, Lambert C, Brinkman FS (January 2005). "PSORTdb: a protein subcellular localization database for bacteria". Nucleic Acids Research. 33 (Database issue): D164–8. doi:10.1093/nar/gki027. PMC 539981. PMID 15608169.
Wu HJ, Ma YK, Chen T, Wang M, Wang XJ (July 2012). "PsRobot: a web-based plant small RNA meta-analysis toolbox". Nucleic Acids Research. 40 (Web Server issue): W22–8. doi:10.1093/nar/gks554. PMC 3394341. PMID 22693224.
Guda C, Subramaniam S (November 2005). "pTARGET [corrected] a new method for predicting protein subcellular localization in eukaryotes". Bioinformatics. 21 (21): 3963–9. doi:10.1093/bioinformatics/bti650. PMID 16144808.
Guda C (July 2006). "pTARGET: a web server for predicting protein subcellular localization". Nucleic Acids Research. 34 (Web Server issue): W210–3. doi:10.1093/nar/gkl093. PMC 1538910. PMID 16844995.
Lee TY, Bo-Kai Hsu J, Chang WC, Huang HD (January 2011). "RegPhos: a system to explore the protein kinase-substrate phosphorylation network in humans". Nucleic Acids Research. 39 (Database issue): D777–87. doi:10.1093/nar/gkq970. PMC 3013804. PMID 21037261.
Elefant N, Berger A, Shein H, Hofree M, Margalit H, Altuvia Y (January 2011). "RepTar: a database of predicted cellular targets of host and viral miRNAs". Nucleic Acids Research. 39 (Database issue): D188–94. doi:10.1093/nar/gkq1233. PMC 3013742. PMID 21149264.
Eggenhofer F, Tafer H, Stadler PF, Hofacker IL (July 2011). "RNApredator: fast accessibility-based prediction of sRNA targets". Nucleic Acids Research. 39 (Web Server issue): W149–54. doi:10.1093/nar/gkr467. PMC 3125805. PMID 21672960.
Shao W, Liu M, Zhang D (January 2016). "Human cell structure-driven model construction for predicting protein subcellular location from biological images". Bioinformatics. 32 (1): 114–21. doi:10.1093/bioinformatics/btv521. PMID 26363175.
Savojardo C, Martelli PL, Fariselli P, Casadio R (February 2017). "SChloro: directing Viridiplantae proteins to six chloroplastic sub-compartments". Bioinformatics. 33 (3): 347–353. doi:10.1093/bioinformatics/btw656. PMC 5408801. PMID 28172591.
Saravanan V, Lakshmi PT (February 2013). "SCLAP: an adaptive boosting method for predicting subchloroplast localization of plant proteins". OMICS. 17 (2): 106–15. doi:10.1089/omi.2012.0070. PMID 23289782.
Mooney C, Wang YH, Pollastri G (October 2011). "SCLpred: protein subcellular localization prediction by N-to-1 neural networks". Bioinformatics. 27 (20): 2812–9. doi:10.1093/bioinformatics/btr494. hdl:10197/3443. PMID 21873639.
Kaleel, M; Zheng, Y; Chen, J; Feng, X; Simpson, JC; Pollastri, G; Mooney, C (6 March 2020). "SCLpred-EMS: subcellular localization prediction of endomembrane system and secretory pathway proteins by Deep N-to-1 Convolutional Neural Networks". Bioinformatics. 36 (11): 3343–3349. doi:10.1093/bioinformatics/btaa156. hdl:10197/12182. PMID 32142105.
Kaleel, Manaz; Ellinger, Liam; Lalor, Clodagh; Pollastri, Gianluca; Mooney, Catherine (2021). "SCLpred-MEM: Subcellular localization prediction of membrane proteins by deep N-to-1 convolutional neural networks". Proteins: Structure, Function, and Bioinformatics. 89 (10): 1233–1239. doi:10.1002/prot.26144. hdl:2346/90320. PMID 33983651. S2CID 234484678.
Bendtsen JD, Jensen LJ, Blom N, Von Heijne G, Brunak S (April 2004). "Feature-based prediction of non-classical and leaderless protein secretion". Protein Engineering, Design & Selection. 17 (4): 349–56. doi:10.1093/protein/gzh037. PMID 15115854.
Bendtsen JD, Kiemer L, Fausbøll A, Brunak S (October 2005). "Non-classical protein secretion in bacteria". BMC Microbiology. 5: 58. doi:10.1186/1471-2180-5-58. PMC 1266369. PMID 16212653.
Xu YY, Yang F, Zhang Y, Shen HB (April 2015). "Bioimaging-based detection of mislocalized proteins in human cancers by semi-supervised learning". Bioinformatics. 31 (7): 1111–9. doi:10.1093/bioinformatics/btu772. PMC 4382902. PMID 25414362.
Shatkay H, Höglund A, Brady S, Blum T, Dönnes P, Kohlbacher O (June 2007). "SherLoc: high-accuracy prediction of protein subcellular localization by integrating text and protein sequence data". Bioinformatics. 23 (11): 1410–7. doi:10.1093/bioinformatics/btm115. PMID 17392328.
Tanz SK, Castleden I, Hooper CM, Vacher M, Small I, Millar HA (January 2013). "SUBA3: a database for integrating experimentation and prediction to define the SUBcellular location of proteins in Arabidopsis". Nucleic Acids Research. 41 (Database issue): D1185–91. doi:10.1093/nar/gks1151. PMC 3531127. PMID 23180787.
Hooper CM, Tanz SK, Castleden IR, Vacher MA, Small ID, Millar AH (December 2014). "SUBAcon: a consensus algorithm for unifying the subcellular localization data of the Arabidopsis proteome". Bioinformatics. 30 (23): 3356–64. doi:10.1093/bioinformatics/btu550. PMID 25150248.
Du P, Cao S, Li Y (November 2009). "SubChlo: predicting protein subchloroplast locations with pseudo-amino acid composition and the evidence-theoretic K-nearest neighbor (ET-KNN) algorithm". Journal of Theoretical Biology. 261 (2): 330–5. Bibcode:2009JThBi.261..330D. doi:10.1016/j.jtbi.2009.08.004. PMID 19679138.
Dunkel M, Günther S, Ahmed J, Wittig B, Preissner R (July 2008). "SuperPred: drug classification and target prediction". Nucleic Acids Research. 36 (Web Server issue): W55–9. doi:10.1093/nar/gkn307. PMC 2447784. PMID 18499712.
Hecker N, Ahmed J, von Eichborn J, Dunkel M, Macha K, Eckert A, Gilson MK, Bourne PE, Preissner R (January 2012). "SuperTarget goes quantitative: update on drug-target interactions". Nucleic Acids Research. 40 (Database issue): D1113–7. doi:10.1093/nar/gkr912. PMC 3245174. PMID 22067455.
Gfeller, David; Michielin, Olivier; Zoete, Vincent (2013-09-17). "Shaping the interaction landscape of bioactive molecules". Bioinformatics. 29 (23): 3073–3079. doi:10.1093/bioinformatics/btt540. ISSN 1460-2059. PMID 24048355.
Gfeller, David; Grosdidier, Aurélien; Wirth, Matthias; Daina, Antoine; Michielin, Olivier; Zoete, Vincent (2014-05-03). "SwissTargetPrediction: a web server for target prediction of bioactive small molecules". Nucleic Acids Research. 42 (W1): W32 – W38. doi:10.1093/nar/gku293. ISSN 1362-4962. PMC 4086140. PMID 24792161.
Lim E, Pon A, Djoumbou Y, Knox C, Shrivastava S, Guo AC, Neveu V, Wishart DS (January 2010). "T3DB: a comprehensively annotated database of common toxins and their targets". Nucleic Acids Research. 38 (Database issue): D781–6. doi:10.1093/nar/gkp934. PMC 2808899. PMID 19897546.
Doyle EL, Booher NJ, Standage DS, Voytas DF, Brendel VP, Vandyk JK, Bogdanove AJ (July 2012). "TAL Effector-Nucleotide Targeter (TALE-NT) 2.0: tools for TAL effector design and target prediction". Nucleic Acids Research. 40 (Web Server issue): W117–22. doi:10.1093/nar/gks608. PMC 3394250. PMID 22693217.
Li H, Gao Z, Kang L, Zhang H, Yang K, Yu K, Luo X, Zhu W, Chen K, Shen J, Wang X, Jiang H (July 2006). "TarFisDock: a web server for identifying drug targets with docking approach". Nucleic Acids Research. 34 (Web Server issue): W219–24. doi:10.1093/nar/gkl114. PMC 1538869. PMID 16844997.
Tjaden B (July 2008). "TargetRNA: a tool for predicting targets of small RNA action in bacteria". Nucleic Acids Research. 36 (Web Server issue): W109–13. doi:10.1093/nar/gkn264. PMC 2447797. PMID 18477632.
Emanuelsson O, Nielsen H, Brunak S, Von Heijne G (July 2000). "Predicting subcellular localization of proteins based on their N-terminal amino acid sequence". Journal of Molecular Biology. 300 (4): 1005–16. doi:10.1006/jmbi.2000.3903. PMID 10891285.
Magariños MP, Carmona SJ, Crowther GJ, Ralph SA, Roos DS, Shanmugam D, Van Voorhis WC, Agüero F (January 2012). "TDR Targets: a chemogenomics resource for neglected diseases". Nucleic Acids Research. 40 (Database issue): D1118–27. doi:10.1093/nar/gkr1053. PMC 3245062. PMID 22116064.
Lin H, Chen W, Yuan LF, Li ZQ, Ding H (June 2013). "Using over-represented tetrapeptides to predict protein submitochondria locations". Acta Biotheoretica. 61 (2): 259–68. doi:10.1007/s10441-013-9181-9. PMID 23475502. S2CID 30809970.
Gromiha MM, Ahmad S, Suwa M (April 2004). "Neural network-based prediction of transmembrane beta-strand segments in outer membrane proteins". Journal of Computational Chemistry. 25 (5): 762–7. doi:10.1002/jcc.10386. PMID 14978719. S2CID 3486330.
Gromiha MM, Ahmad S, Suwa M (July 2005). "TMBETA-NET: discrimination and prediction of membrane spanning beta-strands in outer membrane proteins". Nucleic Acids Research. 33 (Web Server issue): W164–7. doi:10.1093/nar/gki367. PMC 1160128. PMID 15980447.
Krogh, Anders; Larsson, Björn; von Heijne, Gunnar; Sonnhammer, Erik L.L (Jan 2001). "Predicting transmembrane protein topology with a hidden markov model: application to complete genomes". Journal of Molecular Biology. 305 (3): 567–580. doi:10.1006/jmbi.2000.4315. ISSN 0022-2836. PMID 11152613.
Indio V, Martelli PL, Savojardo C, Fariselli P, Casadio R (April 2013). "The prediction of organelle-targeting peptides in eukaryotic proteins with Grammatical-Restrained Hidden Conditional Random Fields". Bioinformatics. 29 (8): 981–8. doi:10.1093/bioinformatics/btt089. PMID 23428638.
Savojardo C, Martelli PL, Fariselli P, Casadio R (October 2015). "TPpred3 detects and discriminates mitochondrial and chloroplastic targeting peptides in eukaryotic proteins". Bioinformatics. 31 (20): 3269–75. doi:10.1093/bioinformatics/btv367. PMID 26079349.
Zhu F, Han B, Kumar P, Liu X, Ma X, Wei X, Huang L, Guo Y, Han L, Zheng C, Chen Y (January 2010). "Update of TTD: Therapeutic Target Database". Nucleic Acids Research. 38 (Database issue): D787–91. doi:10.1093/nar/gkp1014. PMC 2808971. PMID 19933260.
Ellis LB, Gao J, Fenner K, Wackett LP (July 2008). "The University of Minnesota pathway prediction system: predicting metabolic logic". Nucleic Acids Research. 36 (Web Server issue): W427–32. doi:10.1093/nar/gkn315. PMC 2447765. PMID 18524801.
Horton P, Park KJ, Obayashi T, Fujita N, Harada H, Adams-Collier CJ, Nakai K (July 2007). "WoLF PSORT: protein localization predictor". Nucleic Acids Research. 35 (Web Server issue): W585–7. doi:10.1093/nar/gkm259. PMC 1933216. PMID 17517783.
Briesemeister S, Rahnenführer J, Kohlbacher O (July 2010). "YLoc--an interpretable web server for predicting subcellular localization". Nucleic Acids Research. 38 (Web Server issue): W497–502. doi:10.1093/nar/gkq477. PMC 2896088. PMID 20507917.
Blancafort P, Magnenat L, Barbas CF (March 2003). "Scanning the human genome with combinatorial transcription factor libraries". Nature Biotechnology. 21 (3): 269–74. doi:10.1038/nbt794. PMID 12592412. S2CID 9761535.
Dreier B, Fuller RP, Segal DJ, Lund CV, Blancafort P, Huber A, Koksch B, Barbas CF (October 2005). "Development of zinc finger domains for recognition of the 5'-CNN-3' family DNA sequences and their use in the construction of artificial transcription factors". The Journal of Biological Chemistry. 280 (42): 35588–97. doi:10.1074/jbc.M506654200. PMID 16107335.
Dreier B, Segal DJ, Barbas CF (November 2000). "Insights into the molecular recognition of the 5'-GNN-3' family of DNA sequences by zinc finger domains". Journal of Molecular Biology. 303 (4): 489–502. doi:10.1006/jmbi.2000.4133. PMID 11054286. S2CID 11263372.
Mandell JG, Barbas CF (July 2006). "Zinc Finger Tools: custom DNA-binding domains for transcription factors and nucleases". Nucleic Acids Research. 34 (Web Server issue): W516–23. doi:10.1093/nar/gkl209. PMC 1538883. PMID 16845061.
Dreier B, Beerli RR, Segal DJ, Flippin JD, Barbas CF (August 2001). "Development of zinc finger domains for recognition of the 5'-ANN-3' family of DNA sequences and their use in the construction of artificial transcription factors". The Journal of Biological Chemistry. 276 (31): 29466–78. doi:10.1074/jbc.M102604200. PMID 11340073.
Segal DJ, Dreier B, Beerli RR, Barbas CF (March 1999). "Toward controlling gene expression at will: selection and design of zinc finger domains recognizing each of the 5'-GNN-3' DNA target sequences". Proceedings of the National Academy of Sciences of the United States of America. 96 (6): 2758–63. Bibcode:1999PNAS...96.2758S. doi:10.1073/pnas.96.6.2758. PMC 15842. PMID 10077584.

ncbi.nlm.nih.gov

Kaundal R, Saini R, Zhao PX (September 2010). "Combining machine learning and homology-based approaches to accurately predict subcellular localization in Arabidopsis". Plant Physiology. 154 (1): 36–54. doi:10.1104/pp.110.156851. PMC 2938157. PMID 20647376.
Piovesan D, Martelli PL, Fariselli P, Zauli A, Rossi I, Casadio R (July 2011). "BAR-PLUS: the Bologna Annotation Resource Plus for functional and structural annotation of protein sequences". Nucleic Acids Research. 39 (Web Server issue): W197–202. doi:10.1093/nar/gkr292. PMC 3125743. PMID 21622657.
Profiti G, Martelli PL, Casadio R (July 2017). "The Bologna Annotation Resource (BAR 3.0): improving protein functional annotation". Nucleic Acids Research. 45 (W1): W285 – W290. doi:10.1093/nar/gkx330. PMC 5570247. PMID 28453653.
Van Domselaar GH, Stothard P, Shrivastava S, Cruz JA, Guo A, Dong X, Lu P, Szafron D, Greiner R, Wishart DS (July 2005). "BASys: a web server for automated bacterial genome annotation". Nucleic Acids Research. 33 (Web Server issue): W455–9. doi:10.1093/nar/gki593. PMC 1160269. PMID 15980511.
Berven FS, Flikka K, Jensen HB, Eidhammer I (July 2004). "BOMP: a program to predict integral beta-barrel outer membrane proteins encoded within genomes of Gram-negative bacteria". Nucleic Acids Research. 32 (Web Server issue): W394–9. doi:10.1093/nar/gkh351. PMC 441489. PMID 15215418.
Taylor PD, Attwood TK, Flower DR (July 2003). "BPROMPT: A consensus server for membrane protein prediction". Nucleic Acids Research. 31 (13): 3698–700. doi:10.1093/nar/gkg554. PMC 168961. PMID 12824397.
Savojard C, Martelli PL, Fariselli P, Profiti G, Casadio R (July 2018). "BUSCA: an integrative web server to predict subcellular localization of proteins". Nucleic Acids Research. 46 (W1): W459 – W466. doi:10.1093/nar/gky320. PMC 6031068. PMID 29718411.
Yu CS, Lin CJ, Hwang JK (May 2004). "Predicting subcellular localization of proteins for Gram-negative bacteria by support vector machines based on n-peptide compositions". Protein Science. 13 (5): 1402–6. doi:10.1110/ps.03479604. PMC 2286765. PMID 15096640.
Paramasivam N, Linke D (2011). "ClubSub-P: Cluster-Based Subcellular Localization Prediction for Gram-Negative Bacteria and Archaea". Frontiers in Microbiology. 2: 218. doi:10.3389/fmicb.2011.00218. PMC 3210502. PMID 22073040.
Goudenège D, Avner S, Lucchetti-Miganeh C, Barloy-Hubler F (March 2010). "CoBaltDB: Complete bacterial and archaeal orfeomes subcellular localization database and associated resources". BMC Microbiology. 10: 88. doi:10.1186/1471-2180-10-88. PMC 2850352. PMID 20331850.
Coronnello C, Benos PV (July 2013). "ComiR: Combinatorial microRNA target prediction tool". Nucleic Acids Research. 41 (Web Server issue): W159–64. doi:10.1093/nar/gkt379. PMC 3692082. PMID 23703208.
Stärk H, Dallago C, Heinzinger M, Rost B (November 2021). "Light Attention Predicts Protein Location from the Language of Life". Bioinformatics Advances. 1 (1): vbab035. doi:10.1093/bioadv/vbab035. PMC 9710637. PMID 36700108.
Maragkakis M, Reczko M, Simossis VA, Alexiou P, Papadopoulos GL, Dalamagas T, Giannopoulos G, Goumas G, Koukis E, Kourtis K, Vergoulis T, Koziris N, Sellis T, Tsanakas P, Hatzigeorgiou AG (July 2009). "DIANA-microT web server: elucidating microRNA functions through target prediction". Nucleic Acids Research. 37 (Web Server issue): W273–6. doi:10.1093/nar/gkp292. PMC 2703977. PMID 19406924.
Paraskevopoulou MD, Georgakilas G, Kostoulas N, Vlachos IS, Vergoulis T, Reczko M, Filippidis C, Dalamagas T, Hatzigeorgiou AG (July 2013). "DIANA-microT web server v5.0: service integration into miRNA functional analysis workflows". Nucleic Acids Research. 41 (Web Server issue): W169–73. doi:10.1093/nar/gkt393. PMC 3692048. PMID 23680784.
Wishart DS, Knox C, Guo AC, Shrivastava S, Hassanali M, Stothard P, Chang Z, Woolsey J (January 2006). "DrugBank: a comprehensive resource for in silico drug discovery and exploration". Nucleic Acids Research. 34 (Database issue): D668–72. doi:10.1093/nar/gkj067. PMC 1347430. PMID 16381955.
Fucile G, Di Biase D, Nahal H, La G, Khodabandeh S, Chen Y, Easley K, Christendat D, Kelley L, Provart NJ (January 2011). "ePlant and the 3D data display initiative: integrative systems biology on the world wide web". PLOS ONE. 6 (1): e15237. Bibcode:2011PLoSO...615237F. doi:10.1371/journal.pone.0015237. PMC 3018417. PMID 21249219.
Bhasin M, Raghava GP (July 2004). "ESLpred: SVM-based method for subcellular localization of eukaryotic proteins using dipeptide composition and PSI-BLAST". Nucleic Acids Research. 32 (Web Server issue): W414–9. doi:10.1093/nar/gkh350. PMC 441488. PMID 15215421.
Chou KC, Shen HB (April 2010). "A new method for predicting the subcellular localization of eukaryotic proteins with both single and multiple sites: Euk-mPLoc 2.0". PLOS ONE. 5 (4): e9931. Bibcode:2010PLoSO...5.9931C. doi:10.1371/journal.pone.0009931. PMC 2848569. PMID 20368981.
Ye H, Ye L, Kang H, Zhang D, Tao L, Tang K, Liu X, Zhu R, Liu Q, Chen YZ, Li Y, Cao Z (January 2011). "HIT: linking herbal active ingredients to targets". Nucleic Acids Research. 39 (Database issue): D1055–9. doi:10.1093/nar/gkq1165. PMC 3013727. PMID 21097881.
Wang JC, Chu PY, Chen CM, Lin JH (July 2012). "idTarget: a web server for identifying protein targets of small chemical molecules with robust scoring functions and a divide-and-conquer docking approach". Nucleic Acids Research. 40 (Web Server issue): W393–9. doi:10.1093/nar/gks496. PMC 3394295. PMID 22649057.
Lin HN, Chen CT, Sung TY, Ho SY, Hsu WL (December 2009). "Protein subcellular localization prediction of eukaryotes using a knowledge-based approach". BMC Bioinformatics. 10 (Suppl 15): S8. doi:10.1186/1471-2105-10-S15-S8. PMC 2788359. PMID 19958518.
Amaral PP, Clark MB, Gascoigne DK, Dinger ME, Mattick JS (January 2011). "lncRNAdb: a reference database for long noncoding RNAs". Nucleic Acids Research. 39 (Database issue): D146–51. doi:10.1093/nar/gkq1138. PMC 3013714. PMID 21112873.
Nair R, Rost B (July 2003). "LOC3D: annotate sub-cellular localization for protein structures". Nucleic Acids Research. 31 (13): 3337–40. doi:10.1093/nar/gkg514. PMC 168921. PMID 12824321.
Fink JL, Aturaliya RN, Davis MJ, Zhang F, Hanson K, Teasdale MS, Kai C, Kawai J, Carninci P, Hayashizaki Y, Teasdale RD (January 2006). "LOCATE: a mouse protein subcellular localization database". Nucleic Acids Research. 34 (Database issue): D213–7. doi:10.1093/nar/gkj069. PMC 1347432. PMID 16381849.
Rastogi S, Rost B (January 2011). "LocDB: experimental annotations of localization for Homo sapiens and Arabidopsis thaliana". Nucleic Acids Research. 39 (Database issue): D230–4. doi:10.1093/nar/gkq927. PMC 3013784. PMID 21071420.
Nair R, Rost B (July 2004). "LOCnet and LOCtarget: sub-cellular localization for structural genomics targets". Nucleic Acids Research. 32 (Web Server issue): W517–21. doi:10.1093/nar/gkh441. PMC 441579. PMID 15215440.
Goldberg T, Hamp T, Rost B (September 2012). "LocTree2 predicts localization for all domains of life". Bioinformatics. 28 (18): i458 – i465. doi:10.1093/bioinformatics/bts390. PMC 3436817. PMID 22962467.
Goldberg T, Hecht M, Hamp T, Karl T, Yachdav G, Ahmed N, Altermann U, Angerer P, Ansorge S, Balasz K, Bernhofer M, Betz A, Cizmadija L, Do KT, Gerke J, Greil R, Joerdens V, Hastreiter M, Hembach K, Herzog M, Kalemanov M, Kluge M, Meier A, Nasir H, Neumaier U, Prade V, Reeb J, Sorokoumov A, Troshani I, Vorberg S, Waldraff S, Zierer J, Nielsen H, Rost B (July 2014). "LocTree3 prediction of localization". Nucleic Acids Research. 42 (Web Server issue): W350–5. doi:10.1093/nar/gku396. PMC 4086075. PMID 24848019.
Simha R, Briesemeister S, Kohlbacher O, Shatkay H (June 2015). "Protein (multi-)location prediction: utilizing interdependencies via a generative model". Bioinformatics. 31 (12): i365–74. doi:10.1093/bioinformatics/btv264. PMC 4765880. PMID 26072505.
Pierleoni A, Indio V, Savojardo C, Fariselli P, Martelli PL, Casadio R (July 2011). "MemPype: a pipeline for the annotation of eukaryotic membrane proteins". Nucleic Acids Research. 39 (Web Server issue): W375–80. doi:10.1093/nar/gkr282. PMC 3125734. PMID 21543452.
Hausser J, Berninger P, Rodak C, Jantscher Y, Wirth S, Zavolan M (July 2009). "MirZ: an integrated microRNA expression atlas and target prediction resource". Nucleic Acids Research. 37 (Web Server issue): W266–72. doi:10.1093/nar/gkp412. PMC 2703880. PMID 19468042.
King, Brian R; Guda, Chittibabu (2007). "ngLOC: an n-gram-based Bayesian method for estimating the subcellular proteomes of eukaryotes". Genome Biology. 8 (5): R68. doi:10.1186/gb-2007-8-5-r68. ISSN 1465-6906. PMC 1929137. PMID 17472741.
Szafron D, Lu P, Greiner R, Wishart DS, Poulin B, Eisner R, Lu Z, Anvik J, Macdonell C, Fyshe A, Meeuwis D (July 2004). "Proteome Analyst: custom predictions with explanations in a web-based tool for high-throughput proteome annotations". Nucleic Acids Research. 32 (Web Server issue): W365–71. doi:10.1093/nar/gkh485. PMC 441623. PMID 15215412.
Liu X, Ouyang S, Yu B, Liu Y, Huang K, Gong J, Zheng S, Li Z, Li H, Jiang H (July 2010). "PharmMapper server: a web server for potential drug target identification using pharmacophore mapping approach". Nucleic Acids Research. 38 (Web Server issue): W609–14. doi:10.1093/nar/gkq300. PMC 2896160. PMID 20430828.
Tang S, Li T, Cong P, Xiong W, Wang Z, Sun J (July 2013). "PlantLoc: an accurate web server for predicting plant protein subcellular localization by substantiality motif". Nucleic Acids Research. 41 (Web Server issue): W441–7. doi:10.1093/nar/gkt428. PMC 3692052. PMID 23729470.
Bagos PG, Liakopoulos TD, Spyropoulos IC, Hamodrakas SJ (July 2004). "PRED-TMBB: a web server for predicting the topology of beta-barrel outer membrane proteins". Nucleic Acids Research. 32 (Web Server issue): W400–4. doi:10.1093/nar/gkh417. PMC 441555. PMID 15215419.
Bagos PG, Liakopoulos TD, Spyropoulos IC, Hamodrakas SJ (March 2004). "A Hidden Markov Model method, capable of predicting and discriminating beta-barrel outer membrane proteins". BMC Bioinformatics. 5: 29. doi:10.1186/1471-2105-5-29. PMC 385222. PMID 15070403.
Cokol M, Nair R, Rost B (November 2000). "Finding nuclear localization signals". EMBO Reports. 1 (5): 411–5. doi:10.1093/embo-reports/kvd092. PMC 1083765. PMID 11258480.
Yachdav G, Kloppmann E, Kajan L, Hecht M, Goldberg T, Hamp T, Hönigschmid P, Schafferhans A, Roos M, Bernhofer M, Richter L, Ashkenazy H, Punta M, Schlessinger A, Bromberg Y, Schneider R, Vriend G, Sander C, Ben-Tal N, Rost B (July 2014). "PredictProtein--an open resource for online prediction of protein structural and functional features". Nucleic Acids Research. 42 (Web Server issue): W337–43. doi:10.1093/nar/gku366. PMC 4086098. PMID 24799431.
Kaján L, Yachdav G, Vicedo E, Steinegger M, Mirdita M, Angermüller C, Böhm A, Domke S, Ertl J, Mertes C, Reisinger E, Staniewski C, Rost B (2013). "Cloud prediction of protein structure and function with PredictProtein for Debian". BioMed Research International. 2013: 1–6. doi:10.1155/2013/398968. PMC 3732596. PMID 23971032.
Rost B, Liu J (July 2003). "The PredictProtein server". Nucleic Acids Research. 31 (13): 3300–4. doi:10.1093/nar/gkg508. PMC 168915. PMID 12824312.
Rost B, Yachdav G, Liu J (July 2004). "The PredictProtein server". Nucleic Acids Research. 32 (Web Server issue): W321–6. doi:10.1093/nar/gkh377. PMC 441515. PMID 15215403.
Mower JP (July 2009). "The PREP suite: predictive RNA editors for plant mitochondrial genes, chloroplast genes and user-defined alignments". Nucleic Acids Research. 37 (Web Server issue): W253–9. doi:10.1093/nar/gkp337. PMC 2703948. PMID 19433507.
Mower JP (April 2005). "PREP-Mt: predictive RNA editor for plant mitochondrial genes". BMC Bioinformatics. 6: 96. doi:10.1186/1471-2105-6-96. PMC 1087475. PMID 15826309.
Huang WL, Tung CW, Ho SW, Hwang SF, Ho SY (February 2008). "ProLoc-GO: utilizing informative Gene Ontology terms for sequence-based prediction of protein subcellular localization". BMC Bioinformatics. 9: 80. doi:10.1186/1471-2105-9-80. PMC 2262056. PMID 18241343.
Yang B, Sayers S, Xiang Z, He Y (January 2011). "Protegen: a web-based protective antigen database and analysis system". Nucleic Acids Research. 39 (Database issue): D1073–8. doi:10.1093/nar/gkq944. PMC 3013795. PMID 20959289.
Drwal, Malgorzata N.; Banerjee, Priyanka; Dunkel, Mathias; Wettig, Martin R.; Preissner, Robert (2014-05-16). "ProTox: a web server for the in silico prediction of rodent oral toxicity". Nucleic Acids Research. 42 (W1): W53 – W58. doi:10.1093/nar/gku401. ISSN 1362-4962. PMC 4086068. PMID 24838562.
Banerjee, Priyanka; Eckert, Andreas O; Schrey, Anna K; Preissner, Robert (2018-04-30). "ProTox-II: a webserver for the prediction of toxicity of chemicals". Nucleic Acids Research. 46 (W1): W257 – W263. doi:10.1093/nar/gky318. ISSN 0305-1048. PMC 6031011. PMID 29718510.
Yu NY, Wagner JR, Laird MR, Melli G, Rey S, Lo R, Dao P, Sahinalp SC, Ester M, Foster LJ, Brinkman FS (July 2010). "PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes". Bioinformatics. 26 (13): 1608–15. doi:10.1093/bioinformatics/btq249. PMC 2887053. PMID 20472543.
Yu NY, Laird MR, Spencer C, Brinkman FS (January 2011). "PSORTdb--an expanded, auto-updated, user-friendly protein subcellular localization database for Bacteria and Archaea". Nucleic Acids Research. 39 (Database issue): D241–4. doi:10.1093/nar/gkq1093. PMC 3013690. PMID 21071402.
Rey S, Acab M, Gardy JL, Laird MR, deFays K, Lambert C, Brinkman FS (January 2005). "PSORTdb: a protein subcellular localization database for bacteria". Nucleic Acids Research. 33 (Database issue): D164–8. doi:10.1093/nar/gki027. PMC 539981. PMID 15608169.
Wu HJ, Ma YK, Chen T, Wang M, Wang XJ (July 2012). "PsRobot: a web-based plant small RNA meta-analysis toolbox". Nucleic Acids Research. 40 (Web Server issue): W22–8. doi:10.1093/nar/gks554. PMC 3394341. PMID 22693224.
Guda C (July 2006). "pTARGET: a web server for predicting protein subcellular localization". Nucleic Acids Research. 34 (Web Server issue): W210–3. doi:10.1093/nar/gkl093. PMC 1538910. PMID 16844995.
Xinyi Z, Yitong T, Yunhao B, Fei C, Caroline U (July 2024). "Prediction of protein subcellular localization in single cells". bioRxiv. doi:10.1101/2024.07.25.605178. PMC 11291118.
Lee TY, Bo-Kai Hsu J, Chang WC, Huang HD (January 2011). "RegPhos: a system to explore the protein kinase-substrate phosphorylation network in humans". Nucleic Acids Research. 39 (Database issue): D777–87. doi:10.1093/nar/gkq970. PMC 3013804. PMID 21037261.
Elefant N, Berger A, Shein H, Hofree M, Margalit H, Altuvia Y (January 2011). "RepTar: a database of predicted cellular targets of host and viral miRNAs". Nucleic Acids Research. 39 (Database issue): D188–94. doi:10.1093/nar/gkq1233. PMC 3013742. PMID 21149264.
Eggenhofer F, Tafer H, Stadler PF, Hofacker IL (July 2011). "RNApredator: fast accessibility-based prediction of sRNA targets". Nucleic Acids Research. 39 (Web Server issue): W149–54. doi:10.1093/nar/gkr467. PMC 3125805. PMID 21672960.
Savojardo C, Martelli PL, Fariselli P, Casadio R (February 2017). "SChloro: directing Viridiplantae proteins to six chloroplastic sub-compartments". Bioinformatics. 33 (3): 347–353. doi:10.1093/bioinformatics/btw656. PMC 5408801. PMID 28172591.
Bendtsen JD, Kiemer L, Fausbøll A, Brunak S (October 2005). "Non-classical protein secretion in bacteria". BMC Microbiology. 5: 58. doi:10.1186/1471-2180-5-58. PMC 1266369. PMID 16212653.
Xu YY, Yang F, Zhang Y, Shen HB (April 2015). "Bioimaging-based detection of mislocalized proteins in human cancers by semi-supervised learning". Bioinformatics. 31 (7): 1111–9. doi:10.1093/bioinformatics/btu772. PMC 4382902. PMID 25414362.
Tanz SK, Castleden I, Hooper CM, Vacher M, Small I, Millar HA (January 2013). "SUBA3: a database for integrating experimentation and prediction to define the SUBcellular location of proteins in Arabidopsis". Nucleic Acids Research. 41 (Database issue): D1185–91. doi:10.1093/nar/gks1151. PMC 3531127. PMID 23180787.
Dunkel M, Günther S, Ahmed J, Wittig B, Preissner R (July 2008). "SuperPred: drug classification and target prediction". Nucleic Acids Research. 36 (Web Server issue): W55–9. doi:10.1093/nar/gkn307. PMC 2447784. PMID 18499712.
Hecker N, Ahmed J, von Eichborn J, Dunkel M, Macha K, Eckert A, Gilson MK, Bourne PE, Preissner R (January 2012). "SuperTarget goes quantitative: update on drug-target interactions". Nucleic Acids Research. 40 (Database issue): D1113–7. doi:10.1093/nar/gkr912. PMC 3245174. PMID 22067455.
Gfeller, David; Grosdidier, Aurélien; Wirth, Matthias; Daina, Antoine; Michielin, Olivier; Zoete, Vincent (2014-05-03). "SwissTargetPrediction: a web server for target prediction of bioactive small molecules". Nucleic Acids Research. 42 (W1): W32 – W38. doi:10.1093/nar/gku293. ISSN 1362-4962. PMC 4086140. PMID 24792161.
Lim E, Pon A, Djoumbou Y, Knox C, Shrivastava S, Guo AC, Neveu V, Wishart DS (January 2010). "T3DB: a comprehensively annotated database of common toxins and their targets". Nucleic Acids Research. 38 (Database issue): D781–6. doi:10.1093/nar/gkp934. PMC 2808899. PMID 19897546.
Doyle EL, Booher NJ, Standage DS, Voytas DF, Brendel VP, Vandyk JK, Bogdanove AJ (July 2012). "TAL Effector-Nucleotide Targeter (TALE-NT) 2.0: tools for TAL effector design and target prediction". Nucleic Acids Research. 40 (Web Server issue): W117–22. doi:10.1093/nar/gks608. PMC 3394250. PMID 22693217.
Li H, Gao Z, Kang L, Zhang H, Yang K, Yu K, Luo X, Zhu W, Chen K, Shen J, Wang X, Jiang H (July 2006). "TarFisDock: a web server for identifying drug targets with docking approach". Nucleic Acids Research. 34 (Web Server issue): W219–24. doi:10.1093/nar/gkl114. PMC 1538869. PMID 16844997.
Tjaden B (July 2008). "TargetRNA: a tool for predicting targets of small RNA action in bacteria". Nucleic Acids Research. 36 (Web Server issue): W109–13. doi:10.1093/nar/gkn264. PMC 2447797. PMID 18477632.
Magariños MP, Carmona SJ, Crowther GJ, Ralph SA, Roos DS, Shanmugam D, Van Voorhis WC, Agüero F (January 2012). "TDR Targets: a chemogenomics resource for neglected diseases". Nucleic Acids Research. 40 (Database issue): D1118–27. doi:10.1093/nar/gkr1053. PMC 3245062. PMID 22116064.
Gromiha MM, Ahmad S, Suwa M (July 2005). "TMBETA-NET: discrimination and prediction of membrane spanning beta-strands in outer membrane proteins". Nucleic Acids Research. 33 (Web Server issue): W164–7. doi:10.1093/nar/gki367. PMC 1160128. PMID 15980447.
Zhu F, Han B, Kumar P, Liu X, Ma X, Wei X, Huang L, Guo Y, Han L, Zheng C, Chen Y (January 2010). "Update of TTD: Therapeutic Target Database". Nucleic Acids Research. 38 (Database issue): D787–91. doi:10.1093/nar/gkp1014. PMC 2808971. PMID 19933260.
Ellis LB, Gao J, Fenner K, Wackett LP (July 2008). "The University of Minnesota pathway prediction system: predicting metabolic logic". Nucleic Acids Research. 36 (Web Server issue): W427–32. doi:10.1093/nar/gkn315. PMC 2447765. PMID 18524801.
Horton P, Park KJ, Obayashi T, Fujita N, Harada H, Adams-Collier CJ, Nakai K (July 2007). "WoLF PSORT: protein localization predictor". Nucleic Acids Research. 35 (Web Server issue): W585–7. doi:10.1093/nar/gkm259. PMC 1933216. PMID 17517783.
Briesemeister S, Rahnenführer J, Kohlbacher O (July 2010). "YLoc--an interpretable web server for predicting subcellular localization". Nucleic Acids Research. 38 (Web Server issue): W497–502. doi:10.1093/nar/gkq477. PMC 2896088. PMID 20507917.
Mandell JG, Barbas CF (July 2006). "Zinc Finger Tools: custom DNA-binding domains for transcription factors and nucleases". Nucleic Acids Research. 34 (Web Server issue): W516–23. doi:10.1093/nar/gkl209. PMC 1538883. PMID 16845061.
Segal DJ, Dreier B, Beerli RR, Barbas CF (March 1999). "Toward controlling gene expression at will: selection and design of zinc finger domains recognizing each of the 5'-GNN-3' DNA target sequences". Proceedings of the National Academy of Sciences of the United States of America. 96 (6): 2758–63. Bibcode:1999PNAS...96.2758S. doi:10.1073/pnas.96.6.2758. PMC 15842. PMID 10077584.

psu.edu

citeseerx.ist.psu.edu

Nair R, Rost B (December 2003). "Better prediction of sub-cellular localization by combining evolutionary and structural information". Proteins. 53 (4): 917–30. CiteSeerX 10.1.1.217.389. doi:10.1002/prot.10507. PMID 14635133. S2CID 3142627.
Lu Z, Szafron D, Greiner R, Lu P, Wishart DS, Poulin B, Anvik J, Macdonell C, Eisner R (March 2004). "Predicting subcellular localization of proteins using machine-learned classifiers". Bioinformatics. 20 (4): 547–56. CiteSeerX 10.1.1.216.1493. doi:10.1093/bioinformatics/btg447. PMID 14990451.

semanticscholar.org

api.semanticscholar.org

Tantoso E, Li KB (August 2008). "AAIndexLoc: predicting subcellular localization of proteins based on a new representation of sequences using amino acid indices". Amino Acids. 35 (2): 345–53. doi:10.1007/s00726-007-0616-y. PMID 18163182. S2CID 712299.
Saravanan V, Lakshmi PT (December 2013). "APSLAP: an adaptive boosting technique for predicting subcellular localization of apoptosis protein". Acta Biotheoretica. 61 (4): 481–97. doi:10.1007/s10441-013-9197-1. PMID 23982307. S2CID 23858443.
Chou KC, Shen HB (2008-01-01). "Cell-PLoc: a package of Web servers for predicting subcellular localization of proteins in various organisms". Nature Protocols. 3 (2): 153–62. doi:10.1038/nprot.2007.494. PMID 18274516. S2CID 226104.
Yu CS, Chen YC, Lu CH, Hwang JK (August 2006). "Prediction of protein subcellular localization". Proteins. 64 (3): 643–51. doi:10.1002/prot.21018. PMID 16752418. S2CID 24245346.
Nair R, Rost B (December 2003). "Better prediction of sub-cellular localization by combining evolutionary and structural information". Proteins. 53 (4): 917–30. CiteSeerX 10.1.1.217.389. doi:10.1002/prot.10507. PMID 14635133. S2CID 3142627.
Panwar B, Raghava GP (May 2012). "Predicting sub-cellular localization of tRNA synthetases from their primary structures". Amino Acids. 42 (5): 1703–13. doi:10.1007/s00726-011-0872-8. PMID 21400228. S2CID 2996097.
Zhu PP, Li WC, Zhong ZJ, Deng EZ, Ding H, Chen W, Lin H (February 2015). "Predicting the subcellular localization of mycobacterial proteins by incorporating the optimal tripeptides into the general form of pseudo amino acid composition". Molecular BioSystems. 11 (2): 558–63. doi:10.1039/c4mb00645c. PMID 25437899. S2CID 8130819.
Woodcroft BJ, Hammond L, Stow JL, Hamilton NA (November 2009). "Automated organelle-based colocalization in whole-cell imaging". Cytometry. Part A. 75 (11): 941–50. doi:10.1002/cyto.a.20786. PMID 19746416. S2CID 25068671.
Kaleel, Manaz; Ellinger, Liam; Lalor, Clodagh; Pollastri, Gianluca; Mooney, Catherine (2021). "SCLpred-MEM: Subcellular localization prediction of membrane proteins by deep N-to-1 convolutional neural networks". Proteins: Structure, Function, and Bioinformatics. 89 (10): 1233–1239. doi:10.1002/prot.26144. hdl:2346/90320. PMID 33983651. S2CID 234484678.
Lin H, Chen W, Yuan LF, Li ZQ, Ding H (June 2013). "Using over-represented tetrapeptides to predict protein submitochondria locations". Acta Biotheoretica. 61 (2): 259–68. doi:10.1007/s10441-013-9181-9. PMID 23475502. S2CID 30809970.
Gromiha MM, Ahmad S, Suwa M (April 2004). "Neural network-based prediction of transmembrane beta-strand segments in outer membrane proteins". Journal of Computational Chemistry. 25 (5): 762–7. doi:10.1002/jcc.10386. PMID 14978719. S2CID 3486330.
Blancafort P, Magnenat L, Barbas CF (March 2003). "Scanning the human genome with combinatorial transcription factor libraries". Nature Biotechnology. 21 (3): 269–74. doi:10.1038/nbt794. PMID 12592412. S2CID 9761535.
Dreier B, Segal DJ, Barbas CF (November 2000). "Insights into the molecular recognition of the 5'-GNN-3' family of DNA sequences by zinc finger domains". Journal of Molecular Biology. 303 (4): 489–502. doi:10.1006/jmbi.2000.4133. PMID 11054286. S2CID 11263372.

vital-it.ch

embnet.vital-it.ch

Hofmann, K; Stoffel, W (1993). "TMbase—A database of membrane spanning proteins segments" (PDF). Biol Chem Hoppe-Seyler. 374: 166.

worldcat.org

search.worldcat.org

Cserzö, Miklos; Eisenhaber, Frank; Eisenhaber, Birgit; Simon, Istvan (Sep 2002). "On filtering false positive transmembrane protein predictions". Protein Engineering, Design and Selection. 15 (9): 745–752. doi:10.1093/protein/15.9.745. ISSN 1741-0134. PMID 12456873.
Tusnády, Gábor E.; Simon, István (Oct 1998). "Principles governing amino acid composition of integral membrane proteins: application to topology prediction 1 1Edited by J. Thornton". Journal of Molecular Biology. 283 (2): 489–506. doi:10.1006/jmbi.1998.2107. ISSN 0022-2836. PMID 9769220.
Tusnady, G. E.; Simon, I. (2001-09-01). "The HMMTOP transmembrane topology prediction server". Bioinformatics. 17 (9): 849–850. doi:10.1093/bioinformatics/17.9.849. ISSN 1367-4803. PMID 11590105.
King, Brian R; Guda, Chittibabu (2007). "ngLOC: an n-gram-based Bayesian method for estimating the subcellular proteomes of eukaryotes". Genome Biology. 8 (5): R68. doi:10.1186/gb-2007-8-5-r68. ISSN 1465-6906. PMC 1929137. PMID 17472741.
Drwal, Malgorzata N.; Banerjee, Priyanka; Dunkel, Mathias; Wettig, Martin R.; Preissner, Robert (2014-05-16). "ProTox: a web server for the in silico prediction of rodent oral toxicity". Nucleic Acids Research. 42 (W1): W53 – W58. doi:10.1093/nar/gku401. ISSN 1362-4962. PMC 4086068. PMID 24838562.
Banerjee, Priyanka; Eckert, Andreas O; Schrey, Anna K; Preissner, Robert (2018-04-30). "ProTox-II: a webserver for the prediction of toxicity of chemicals". Nucleic Acids Research. 46 (W1): W257 – W263. doi:10.1093/nar/gky318. ISSN 0305-1048. PMC 6031011. PMID 29718510.
Gfeller, David; Michielin, Olivier; Zoete, Vincent (2013-09-17). "Shaping the interaction landscape of bioactive molecules". Bioinformatics. 29 (23): 3073–3079. doi:10.1093/bioinformatics/btt540. ISSN 1460-2059. PMID 24048355.
Gfeller, David; Grosdidier, Aurélien; Wirth, Matthias; Daina, Antoine; Michielin, Olivier; Zoete, Vincent (2014-05-03). "SwissTargetPrediction: a web server for target prediction of bioactive small molecules". Nucleic Acids Research. 42 (W1): W32 – W38. doi:10.1093/nar/gku293. ISSN 1362-4962. PMC 4086140. PMID 24792161.
Krogh, Anders; Larsson, Björn; von Heijne, Gunnar; Sonnhammer, Erik L.L (Jan 2001). "Predicting transmembrane protein topology with a hidden markov model: application to complete genomes". Journal of Molecular Biology. 305 (3): 567–580. doi:10.1006/jmbi.2000.4315. ISSN 0022-2836. PMID 11152613.