Structural alignment (English Wikipedia)

Analysis of information sources in references of the Wikipedia article "Structural alignment" in English language version.

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3semanticscholar.org

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1nbn-resolving.de

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doi.org

Kryshtafovych A, Monastyrskyy B, Fidelis K (2016). "CASP11 statistics and the prediction center evaluation system. \". Proteins. 84 (Suppl 1): (Suppl 1):15–19. doi:10.1002/prot.25005. PMC 5479680. PMID 26857434.
Lars Malmström Michael Riffle; Charlie EM Strauss; Dylan Chivian; Trisha N Davis; Richard Bonneau; David Baker (2007). "Superfamily Assignments for the Yeast Proteome through Integration of Structure Prediction with the Gene Ontology". PLOS Biol. 5 (4): e76corresponding author1, 2. doi:10.1371/journal.pbio.0050076. PMC 1828141. PMID 17373854.
David E. Kim; Dylan Chivian; David Baker (2004). "Protein structure prediction and analysis using the Robetta server". Nucleic Acids Research. 32(Web Server issue): W526–W531 (Web Server issue): W526–W531. doi:10.1093/nar/gkh468. PMC 441606. PMID 15215442.
Zhang Y, Skolnick J (2005). "The protein structure prediction problem could be solved using the current PDB library". Proc Natl Acad Sci USA. 102 (4): 1029–34. Bibcode:2005PNAS..102.1029Z. doi:10.1073/pnas.0407152101. PMC 545829. PMID 15653774.
Zemla A. (2003). "LGA — A Method for Finding 3-D Similarities in Protein Structures". Nucleic Acids Research. 31 (13): 3370–3374. doi:10.1093/nar/gkg571. PMC 168977. PMID 12824330.
Godzik A (1996). "The structural alignment between two proteins: Is there a unique answer?". Protein Science. 5 (7): 1325–38. doi:10.1002/pro.5560050711. PMC 2143456. PMID 8819165.
Martin ACR (1982). "Rapid Comparison of Protein Structures". Acta Crystallogr A. 38 (6): 871–873. Bibcode:1982AcCrA..38..871M. doi:10.1107/S0567739482001806.
Theobald DL, Wuttke DS (2006). "Empirical Bayes hierarchical models for regularizing maximum likelihood estimation in the matrix Gaussian Procrustes problem". Proceedings of the National Academy of Sciences. 103 (49): 18521–18527. Bibcode:2006PNAS..10318521T. doi:10.1073/pnas.0508445103. PMC 1664551. PMID 17130458.
Theobald DL, Wuttke DS (2006). "THESEUS: Maximum likelihood superpositioning and analysis of macromolecular structures". Bioinformatics. 22 (17): 2171–2172. doi:10.1093/bioinformatics/btl332. PMC 2584349. PMID 16777907.
Diederichs K. (1995). "Structural superposition of proteins with unknown alignment and detection of topological similarity using a six-dimensional search algorithm". Proteins. 23 (2): 187–95. doi:10.1002/prot.340230208. PMID 8592700. S2CID 3469775.
Maiti R, Van Domselaar GH, Zhang H, Wishart DS (2004). "SuperPose: a simple server for sophisticated structural superposition". Nucleic Acids Res. 32 (Web Server issue): W590–4. doi:10.1093/nar/gkh477. PMC 441615. PMID 15215457.
Ortiz, AR; Strauss CE; Olmea O. (2002). "MAMMOTH (matching molecular models obtained from theory): an automated method for model comparison". Protein Science. 11 (11): 2606–2621. doi:10.1110/ps.0215902. PMC 2373724. PMID 12381844.
Zhang Y, Skolnick J (2004). "Scoring function for automated assessment of protein structure template quality". Proteins. 57 (4): 702–710. doi:10.1002/prot.20264. PMID 15476259. S2CID 7954787.
Siew N, Elofsson A, Rychlewsk L, Fischer D (2000). "MaxSub: an automated measure for the assessment of protein structure prediction quality". Bioinformatics. 16 (9): 776–85. doi:10.1093/bioinformatics/16.9.776. PMID 11108700.
Poleksic A (2009). "Algorithms for optimal protein structure alignment". Bioinformatics. 25 (21): 2751–2756. doi:10.1093/bioinformatics/btp530. PMID 19734152.
Lathrop RH. (1994). "The protein threading problem with sequence amino acid interaction preferences is NP-complete". Protein Eng. 7 (9): 1059–68. CiteSeerX 10.1.1.367.9081. doi:10.1093/protein/7.9.1059. PMID 7831276.
Wang L, Jiang T (1994). "On the complexity of multiple sequence alignment". Journal of Computational Biology. 1 (4): 337–48. CiteSeerX 10.1.1.408.894. doi:10.1089/cmb.1994.1.337. PMID 8790475.
Kolodny R, Linial N (2004). "Approximate protein structural alignment in polynomial time". PNAS. 101 (33): 12201–12206. doi:10.1073/pnas.0404383101. PMC 514457. PMID 15304646.
Martinez L, Andreani, R, Martinez, JM. (2007). "Convergent algorithms for protein structural alignment". BMC Bioinformatics. 8: 306. doi:10.1186/1471-2105-8-306. PMC 1995224. PMID 17714583.{{cite journal}}: CS1 maint: multiple names: authors list (link)
Holm L, Sander C (1996). "Mapping the protein universe". Science. 273 (5275): 595–603. Bibcode:1996Sci...273..595H. doi:10.1126/science.273.5275.595. PMID 8662544. S2CID 7509134.
Shindyalov, I.N.; Bourne P.E. (1998). "Protein structure alignment by incremental combinatorial extension (CE) of the optimal path". Protein Engineering. 11 (9): 739–747. doi:10.1093/protein/11.9.739. PMID 9796821.
Prlic A, Bliven S, Rose PW, Bluhm WF, Bizon C, Godzik A, Bourne PE (2010). "Pre-calculated protein structure alignments at the RCSB PDB website". Bioinformatics. 26 (23): 2983–2985. doi:10.1093/bioinformatics/btq572. PMC 3003546. PMID 20937596.
Pin-Hao Chi; Bin Pang; Dmitry Korkin; Chi-Ren Shyu (2009). "Efficient SCOP-fold classification and retrieval using index-based protein substructure alignments". Bioinformatics. 25 (19): 2559–2565. doi:10.1093/bioinformatics/btp474. PMID 19667079.
Sara Cheek; Yuan Qi; Sri Krishna; Lisa N Kinch; Nick V Grishin (2004). "SCOPmap: Automated assignment of protein structures to evolutionary superfamilies". BMC Bioinformatics. 5 (197): 197. doi:10.1186/1471-2105-5-197. PMC 544345. PMID 15598351.
Kai Wang; Ram Samudrala (2005). "FSSA: a novel method for identifying functional signatures from structural alignments". Bioinformatics. 21 (13): 2969–2977. doi:10.1093/bioinformatics/bti471. PMID 15860561.
Taylor WR, Flores TP, Orengo CA (1994). "Multiple protein structure alignment". Protein Sci. 3 (10): 1858–70. doi:10.1002/pro.5560031025. PMC 2142613. PMID 7849601.
Orengo CA, Michie AD, Jones S, Jones DT, Swindells MB, Thornton JM (1997). "CATH: A hierarchical classification of protein domain structures". Structure. 5 (8): 1093–1108. doi:10.1016/S0969-2126(97)00260-8. PMID 9309224.
Zhang Y, Skolnick J (2005). "TM-align: A protein structure alignment algorithm based on the TM-score". Nucleic Acids Research. 33 (7): 2302–2309. doi:10.1093/nar/gki524. PMC 1084323. PMID 15849316.
Stefano Angaran; Mary Ellen Bock; Claudio Garutti; Concettina Guerra1 (2009). "MolLoc: a web tool for the local structural alignment of molecular surfaces". Nucleic Acids Research. 37 (Web Server issue): W565–70. doi:10.1093/nar/gkp405. PMC 2703929. PMID 19465382.{{cite journal}}: CS1 maint: numeric names: authors list (link)
Gaëlle Debret; Arnaud Martel; Philippe Cuniasse (2009). "RASMOT-3D PRO: a 3D motif search webserver". Nucleic Acids Research. 37 (Web Server issue): W459–64. doi:10.1093/nar/gkp304. PMC 2703991. PMID 19417073.
Alexandra Shulman-Peleg; Maxim Shatsky; Ruth Nussinov; Haim J. Wolfson (2008). "MultiBind and MAPPIS: webservers for multiple alignment of protein 3D-binding sites and their interactions". Nucleic Acids Research. 36 (Web Server issue): W260–4. doi:10.1093/nar/gkn185. PMC 2447750. PMID 18467424.
Alexandra Shulman-Peleg; Maxim Shatsky; Ruth Nussinov; Haim J Wolfson (2007). "Spatial chemical conservation of hot spot interactions in protein-protein complexes". BMC Biology. 5 (43): 43. doi:10.1186/1741-7007-5-43. PMC 2231411. PMID 17925020.
Gabriele Ausiello; Pier Federico Gherardini; Paolo Marcatili; Anna Tramontano; Allegra Via; Manuela Helmer-Citterich (2008). "FunClust: a web server for the identification of structural motifs in a set of non-homologous protein structures". BMC Biology. 9 (Suppl 2): S2. doi:10.1186/1471-2105-9-S2-S2. PMC 2323665. PMID 18387204.
Janez Konc; Dušanka Janežič (2010). "ProBiS algorithm for detection of structurally similar protein binding sites by local structural alignment". Bioinformatics. 26 (9): 1160–1168. doi:10.1093/bioinformatics/btq100. PMC 2859123. PMID 20305268.
Hui Sun Lee; Wonpil Im (2012). "Identification of Ligand Templates using Local Structure Alignment for Structure-Based Drug Design". Journal of Chemical Information and Modeling. 52 (10): 2784–2795. doi:10.1021/ci300178e. PMC 3478504. PMID 22978550.
Hui Sun Lee; Wonpil Im (2013). "Ligand Binding Site Detection by Local Structure Alignment and Its Performance Complementarity". Journal of Chemical Information and Modeling. 53 (9): 2462–2470. doi:10.1021/ci4003602. PMC 3821077. PMID 23957286.
Barthel D., Hirst J.D., Blazewicz J., Burke E.K. and Krasnogor N. (2007). "ProCKSI: a decision support system for Protein (Structure) Comparison, Knowledge, Similarity and Information". BMC Bioinformatics. 8: 416. doi:10.1186/1471-2105-8-416. PMC 2222653. PMID 17963510.{{cite journal}}: CS1 maint: multiple names: authors list (link)
Sippl, M.; Wiederstein, M. (2012). "Detection of spatial correlations in protein structures and molecular complexes". Structure. 20 (4): 718–728. doi:10.1016/j.str.2012.01.024. PMC 3320710. PMID 22483118.
Torarinsson E, Sawera M, Havgaard JH, Fredholm M, Gorodkin J (2006). "Thousands of corresponding human and mouse genomic regions unalignable in primary sequence contain common RNA structure". Genome Res. 16 (7): 885–9. doi:10.1101/gr.5226606. PMC 1484455. PMID 16751343.
Hoksza D, Svozil D (2012). "Efficient RNA pairwise structure comparison by SETTER method". Bioinformatics. 28 (14): 1858–1864. doi:10.1093/bioinformatics/bts301. PMID 22611129.
Cech P, Svozil D, Hoksza D (2012). "SETTER: web server for RNA structure comparison". Nucleic Acids Research. 40 (W1): W42–W48. doi:10.1093/nar/gks560. PMC 3394248. PMID 22693209.
Havgaard JH, Lyngso RB, Stormo GD, Gorodkin J (2005). "Pairwise local structural alignment of RNA sequences with sequence similarity less than 40%". Bioinformatics. 21 (9): 1815–24. doi:10.1093/bioinformatics/bti279. PMID 15657094.
Mathews DH, Turner DH (2006). "Prediction of RNA secondary structure by free energy minimization". Curr Opin Struct Biol. 16 (3): 270–8. doi:10.1016/j.sbi.2006.05.010. PMID 16713706.

harvard.edu

ui.adsabs.harvard.edu

Zhang Y, Skolnick J (2005). "The protein structure prediction problem could be solved using the current PDB library". Proc Natl Acad Sci USA. 102 (4): 1029–34. Bibcode:2005PNAS..102.1029Z. doi:10.1073/pnas.0407152101. PMC 545829. PMID 15653774.
Martin ACR (1982). "Rapid Comparison of Protein Structures". Acta Crystallogr A. 38 (6): 871–873. Bibcode:1982AcCrA..38..871M. doi:10.1107/S0567739482001806.
Theobald DL, Wuttke DS (2006). "Empirical Bayes hierarchical models for regularizing maximum likelihood estimation in the matrix Gaussian Procrustes problem". Proceedings of the National Academy of Sciences. 103 (49): 18521–18527. Bibcode:2006PNAS..10318521T. doi:10.1073/pnas.0508445103. PMC 1664551. PMID 17130458.
Holm L, Sander C (1996). "Mapping the protein universe". Science. 273 (5275): 595–603. Bibcode:1996Sci...273..595H. doi:10.1126/science.273.5275.595. PMID 8662544. S2CID 7509134.

nbn-resolving.de

Diederichs K. (1995). "Structural superposition of proteins with unknown alignment and detection of topological similarity using a six-dimensional search algorithm". Proteins. 23 (2): 187–95. doi:10.1002/prot.340230208. PMID 8592700. S2CID 3469775.

nih.gov

pubmed.ncbi.nlm.nih.gov

Kryshtafovych A, Monastyrskyy B, Fidelis K (2016). "CASP11 statistics and the prediction center evaluation system. \". Proteins. 84 (Suppl 1): (Suppl 1):15–19. doi:10.1002/prot.25005. PMC 5479680. PMID 26857434.
Lars Malmström Michael Riffle; Charlie EM Strauss; Dylan Chivian; Trisha N Davis; Richard Bonneau; David Baker (2007). "Superfamily Assignments for the Yeast Proteome through Integration of Structure Prediction with the Gene Ontology". PLOS Biol. 5 (4): e76corresponding author1, 2. doi:10.1371/journal.pbio.0050076. PMC 1828141. PMID 17373854.
David E. Kim; Dylan Chivian; David Baker (2004). "Protein structure prediction and analysis using the Robetta server". Nucleic Acids Research. 32(Web Server issue): W526–W531 (Web Server issue): W526–W531. doi:10.1093/nar/gkh468. PMC 441606. PMID 15215442.
Zhang Y, Skolnick J (2005). "The protein structure prediction problem could be solved using the current PDB library". Proc Natl Acad Sci USA. 102 (4): 1029–34. Bibcode:2005PNAS..102.1029Z. doi:10.1073/pnas.0407152101. PMC 545829. PMID 15653774.
Zemla A. (2003). "LGA — A Method for Finding 3-D Similarities in Protein Structures". Nucleic Acids Research. 31 (13): 3370–3374. doi:10.1093/nar/gkg571. PMC 168977. PMID 12824330.
Godzik A (1996). "The structural alignment between two proteins: Is there a unique answer?". Protein Science. 5 (7): 1325–38. doi:10.1002/pro.5560050711. PMC 2143456. PMID 8819165.
Theobald DL, Wuttke DS (2006). "Empirical Bayes hierarchical models for regularizing maximum likelihood estimation in the matrix Gaussian Procrustes problem". Proceedings of the National Academy of Sciences. 103 (49): 18521–18527. Bibcode:2006PNAS..10318521T. doi:10.1073/pnas.0508445103. PMC 1664551. PMID 17130458.
Theobald DL, Wuttke DS (2006). "THESEUS: Maximum likelihood superpositioning and analysis of macromolecular structures". Bioinformatics. 22 (17): 2171–2172. doi:10.1093/bioinformatics/btl332. PMC 2584349. PMID 16777907.
Diederichs K. (1995). "Structural superposition of proteins with unknown alignment and detection of topological similarity using a six-dimensional search algorithm". Proteins. 23 (2): 187–95. doi:10.1002/prot.340230208. PMID 8592700. S2CID 3469775.
Maiti R, Van Domselaar GH, Zhang H, Wishart DS (2004). "SuperPose: a simple server for sophisticated structural superposition". Nucleic Acids Res. 32 (Web Server issue): W590–4. doi:10.1093/nar/gkh477. PMC 441615. PMID 15215457.
Ortiz, AR; Strauss CE; Olmea O. (2002). "MAMMOTH (matching molecular models obtained from theory): an automated method for model comparison". Protein Science. 11 (11): 2606–2621. doi:10.1110/ps.0215902. PMC 2373724. PMID 12381844.
Zhang Y, Skolnick J (2004). "Scoring function for automated assessment of protein structure template quality". Proteins. 57 (4): 702–710. doi:10.1002/prot.20264. PMID 15476259. S2CID 7954787.
Siew N, Elofsson A, Rychlewsk L, Fischer D (2000). "MaxSub: an automated measure for the assessment of protein structure prediction quality". Bioinformatics. 16 (9): 776–85. doi:10.1093/bioinformatics/16.9.776. PMID 11108700.
Poleksic A (2009). "Algorithms for optimal protein structure alignment". Bioinformatics. 25 (21): 2751–2756. doi:10.1093/bioinformatics/btp530. PMID 19734152.
Lathrop RH. (1994). "The protein threading problem with sequence amino acid interaction preferences is NP-complete". Protein Eng. 7 (9): 1059–68. CiteSeerX 10.1.1.367.9081. doi:10.1093/protein/7.9.1059. PMID 7831276.
Wang L, Jiang T (1994). "On the complexity of multiple sequence alignment". Journal of Computational Biology. 1 (4): 337–48. CiteSeerX 10.1.1.408.894. doi:10.1089/cmb.1994.1.337. PMID 8790475.
Kolodny R, Linial N (2004). "Approximate protein structural alignment in polynomial time". PNAS. 101 (33): 12201–12206. doi:10.1073/pnas.0404383101. PMC 514457. PMID 15304646.
Martinez L, Andreani, R, Martinez, JM. (2007). "Convergent algorithms for protein structural alignment". BMC Bioinformatics. 8: 306. doi:10.1186/1471-2105-8-306. PMC 1995224. PMID 17714583.{{cite journal}}: CS1 maint: multiple names: authors list (link)
Holm L, Sander C (1996). "Mapping the protein universe". Science. 273 (5275): 595–603. Bibcode:1996Sci...273..595H. doi:10.1126/science.273.5275.595. PMID 8662544. S2CID 7509134.
Shindyalov, I.N.; Bourne P.E. (1998). "Protein structure alignment by incremental combinatorial extension (CE) of the optimal path". Protein Engineering. 11 (9): 739–747. doi:10.1093/protein/11.9.739. PMID 9796821.
Prlic A, Bliven S, Rose PW, Bluhm WF, Bizon C, Godzik A, Bourne PE (2010). "Pre-calculated protein structure alignments at the RCSB PDB website". Bioinformatics. 26 (23): 2983–2985. doi:10.1093/bioinformatics/btq572. PMC 3003546. PMID 20937596.
Pin-Hao Chi; Bin Pang; Dmitry Korkin; Chi-Ren Shyu (2009). "Efficient SCOP-fold classification and retrieval using index-based protein substructure alignments". Bioinformatics. 25 (19): 2559–2565. doi:10.1093/bioinformatics/btp474. PMID 19667079.
Sara Cheek; Yuan Qi; Sri Krishna; Lisa N Kinch; Nick V Grishin (2004). "SCOPmap: Automated assignment of protein structures to evolutionary superfamilies". BMC Bioinformatics. 5 (197): 197. doi:10.1186/1471-2105-5-197. PMC 544345. PMID 15598351.
Kai Wang; Ram Samudrala (2005). "FSSA: a novel method for identifying functional signatures from structural alignments". Bioinformatics. 21 (13): 2969–2977. doi:10.1093/bioinformatics/bti471. PMID 15860561.
Taylor WR, Flores TP, Orengo CA (1994). "Multiple protein structure alignment". Protein Sci. 3 (10): 1858–70. doi:10.1002/pro.5560031025. PMC 2142613. PMID 7849601.
Orengo CA, Michie AD, Jones S, Jones DT, Swindells MB, Thornton JM (1997). "CATH: A hierarchical classification of protein domain structures". Structure. 5 (8): 1093–1108. doi:10.1016/S0969-2126(97)00260-8. PMID 9309224.
Zhang Y, Skolnick J (2005). "TM-align: A protein structure alignment algorithm based on the TM-score". Nucleic Acids Research. 33 (7): 2302–2309. doi:10.1093/nar/gki524. PMC 1084323. PMID 15849316.
Stefano Angaran; Mary Ellen Bock; Claudio Garutti; Concettina Guerra1 (2009). "MolLoc: a web tool for the local structural alignment of molecular surfaces". Nucleic Acids Research. 37 (Web Server issue): W565–70. doi:10.1093/nar/gkp405. PMC 2703929. PMID 19465382.{{cite journal}}: CS1 maint: numeric names: authors list (link)
Gaëlle Debret; Arnaud Martel; Philippe Cuniasse (2009). "RASMOT-3D PRO: a 3D motif search webserver". Nucleic Acids Research. 37 (Web Server issue): W459–64. doi:10.1093/nar/gkp304. PMC 2703991. PMID 19417073.
Alexandra Shulman-Peleg; Maxim Shatsky; Ruth Nussinov; Haim J. Wolfson (2008). "MultiBind and MAPPIS: webservers for multiple alignment of protein 3D-binding sites and their interactions". Nucleic Acids Research. 36 (Web Server issue): W260–4. doi:10.1093/nar/gkn185. PMC 2447750. PMID 18467424.
Alexandra Shulman-Peleg; Maxim Shatsky; Ruth Nussinov; Haim J Wolfson (2007). "Spatial chemical conservation of hot spot interactions in protein-protein complexes". BMC Biology. 5 (43): 43. doi:10.1186/1741-7007-5-43. PMC 2231411. PMID 17925020.
Gabriele Ausiello; Pier Federico Gherardini; Paolo Marcatili; Anna Tramontano; Allegra Via; Manuela Helmer-Citterich (2008). "FunClust: a web server for the identification of structural motifs in a set of non-homologous protein structures". BMC Biology. 9 (Suppl 2): S2. doi:10.1186/1471-2105-9-S2-S2. PMC 2323665. PMID 18387204.
Janez Konc; Dušanka Janežič (2010). "ProBiS algorithm for detection of structurally similar protein binding sites by local structural alignment". Bioinformatics. 26 (9): 1160–1168. doi:10.1093/bioinformatics/btq100. PMC 2859123. PMID 20305268.
Hui Sun Lee; Wonpil Im (2012). "Identification of Ligand Templates using Local Structure Alignment for Structure-Based Drug Design". Journal of Chemical Information and Modeling. 52 (10): 2784–2795. doi:10.1021/ci300178e. PMC 3478504. PMID 22978550.
Hui Sun Lee; Wonpil Im (2013). "Ligand Binding Site Detection by Local Structure Alignment and Its Performance Complementarity". Journal of Chemical Information and Modeling. 53 (9): 2462–2470. doi:10.1021/ci4003602. PMC 3821077. PMID 23957286.
Barthel D., Hirst J.D., Blazewicz J., Burke E.K. and Krasnogor N. (2007). "ProCKSI: a decision support system for Protein (Structure) Comparison, Knowledge, Similarity and Information". BMC Bioinformatics. 8: 416. doi:10.1186/1471-2105-8-416. PMC 2222653. PMID 17963510.{{cite journal}}: CS1 maint: multiple names: authors list (link)
Sippl, M.; Wiederstein, M. (2012). "Detection of spatial correlations in protein structures and molecular complexes". Structure. 20 (4): 718–728. doi:10.1016/j.str.2012.01.024. PMC 3320710. PMID 22483118.
Torarinsson E, Sawera M, Havgaard JH, Fredholm M, Gorodkin J (2006). "Thousands of corresponding human and mouse genomic regions unalignable in primary sequence contain common RNA structure". Genome Res. 16 (7): 885–9. doi:10.1101/gr.5226606. PMC 1484455. PMID 16751343.
Hoksza D, Svozil D (2012). "Efficient RNA pairwise structure comparison by SETTER method". Bioinformatics. 28 (14): 1858–1864. doi:10.1093/bioinformatics/bts301. PMID 22611129.
Cech P, Svozil D, Hoksza D (2012). "SETTER: web server for RNA structure comparison". Nucleic Acids Research. 40 (W1): W42–W48. doi:10.1093/nar/gks560. PMC 3394248. PMID 22693209.
Havgaard JH, Lyngso RB, Stormo GD, Gorodkin J (2005). "Pairwise local structural alignment of RNA sequences with sequence similarity less than 40%". Bioinformatics. 21 (9): 1815–24. doi:10.1093/bioinformatics/bti279. PMID 15657094.
Mathews DH, Turner DH (2006). "Prediction of RNA secondary structure by free energy minimization". Curr Opin Struct Biol. 16 (3): 270–8. doi:10.1016/j.sbi.2006.05.010. PMID 16713706.

ncbi.nlm.nih.gov

Kryshtafovych A, Monastyrskyy B, Fidelis K (2016). "CASP11 statistics and the prediction center evaluation system. \". Proteins. 84 (Suppl 1): (Suppl 1):15–19. doi:10.1002/prot.25005. PMC 5479680. PMID 26857434.
Lars Malmström Michael Riffle; Charlie EM Strauss; Dylan Chivian; Trisha N Davis; Richard Bonneau; David Baker (2007). "Superfamily Assignments for the Yeast Proteome through Integration of Structure Prediction with the Gene Ontology". PLOS Biol. 5 (4): e76corresponding author1, 2. doi:10.1371/journal.pbio.0050076. PMC 1828141. PMID 17373854.
David E. Kim; Dylan Chivian; David Baker (2004). "Protein structure prediction and analysis using the Robetta server". Nucleic Acids Research. 32(Web Server issue): W526–W531 (Web Server issue): W526–W531. doi:10.1093/nar/gkh468. PMC 441606. PMID 15215442.
Zhang Y, Skolnick J (2005). "The protein structure prediction problem could be solved using the current PDB library". Proc Natl Acad Sci USA. 102 (4): 1029–34. Bibcode:2005PNAS..102.1029Z. doi:10.1073/pnas.0407152101. PMC 545829. PMID 15653774.
Zemla A. (2003). "LGA — A Method for Finding 3-D Similarities in Protein Structures". Nucleic Acids Research. 31 (13): 3370–3374. doi:10.1093/nar/gkg571. PMC 168977. PMID 12824330.
Godzik A (1996). "The structural alignment between two proteins: Is there a unique answer?". Protein Science. 5 (7): 1325–38. doi:10.1002/pro.5560050711. PMC 2143456. PMID 8819165.
Theobald DL, Wuttke DS (2006). "Empirical Bayes hierarchical models for regularizing maximum likelihood estimation in the matrix Gaussian Procrustes problem". Proceedings of the National Academy of Sciences. 103 (49): 18521–18527. Bibcode:2006PNAS..10318521T. doi:10.1073/pnas.0508445103. PMC 1664551. PMID 17130458.
Theobald DL, Wuttke DS (2006). "THESEUS: Maximum likelihood superpositioning and analysis of macromolecular structures". Bioinformatics. 22 (17): 2171–2172. doi:10.1093/bioinformatics/btl332. PMC 2584349. PMID 16777907.
Maiti R, Van Domselaar GH, Zhang H, Wishart DS (2004). "SuperPose: a simple server for sophisticated structural superposition". Nucleic Acids Res. 32 (Web Server issue): W590–4. doi:10.1093/nar/gkh477. PMC 441615. PMID 15215457.
Ortiz, AR; Strauss CE; Olmea O. (2002). "MAMMOTH (matching molecular models obtained from theory): an automated method for model comparison". Protein Science. 11 (11): 2606–2621. doi:10.1110/ps.0215902. PMC 2373724. PMID 12381844.
Kolodny R, Linial N (2004). "Approximate protein structural alignment in polynomial time". PNAS. 101 (33): 12201–12206. doi:10.1073/pnas.0404383101. PMC 514457. PMID 15304646.
Martinez L, Andreani, R, Martinez, JM. (2007). "Convergent algorithms for protein structural alignment". BMC Bioinformatics. 8: 306. doi:10.1186/1471-2105-8-306. PMC 1995224. PMID 17714583.{{cite journal}}: CS1 maint: multiple names: authors list (link)
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