References analysis of the Wikipedia article "Docking (molecular)" in the English version

doi.org

Lengauer T, Rarey M (Jun 1996). "Computational methods for biomolecular docking". Current Opinion in Structural Biology. 6 (3): 402–6. doi:10.1016/S0959-440X(96)80061-3. PMID 8804827.

Kitchen DB, Decornez H, Furr JR, Bajorath J (Nov 2004). "Docking and scoring in virtual screening for drug discovery: methods and applications". Nature Reviews. Drug Discovery. 3 (11): 935–49. doi:10.1038/nrd1549. PMID 15520816. S2CID 1069493.

Mostashari-Rad T, Arian R, Mehridehnavi A, Fassihi A, Ghasemi F (June 13, 2019). "Study of CXCR4 chemokine receptor inhibitors using QSPR andmolecular docking methodologies". Journal of Theoretical and Computational Chemistry. 178 (4). doi:10.1142/S0219633619500184. S2CID 164985789.

Jorgensen WL (Nov 1991). "Rusting of the lock and key model for protein-ligand binding". Science. 254 (5034): 954–5. Bibcode:1991Sci...254..954J. doi:10.1126/science.1719636. PMID 1719636.

Wei BQ, Weaver LH, Ferrari AM, Matthews BW, Shoichet BK (Apr 2004). "Testing a flexible-receptor docking algorithm in a model binding site". Journal of Molecular Biology. 337 (5): 1161–82. doi:10.1016/j.jmb.2004.02.015. PMID 15046985.

Goldman BB, Wipke WT (2000). "QSD quadratic shape descriptors. 2. Molecular docking using quadratic shape descriptors (QSDock)". Proteins. 38 (1): 79–94. doi:10.1002/(SICI)1097-0134(20000101)38:1<79::AID-PROT9>3.0.CO;2-U. PMID 10651041.

Meng EC, Shoichet BK, Kuntz ID (1992). "Automated docking with grid-based energy evaluation". Journal of Computational Chemistry. 13 (4): 505–524. doi:10.1002/jcc.540130412. S2CID 97778840.

Morris GM, Goodsell DS, Halliday RS, Huey R, Hart WE, Belew RK, Olson AJ (1998). "Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function". Journal of Computational Chemistry. 19 (14): 1639–1662. CiteSeerX 10.1.1.471.5900. doi:10.1002/(SICI)1096-987X(19981115)19:14<1639::AID-JCC10>3.0.CO;2-B.

Feig M, Onufriev A, Lee MS, Im W, Case DA, Brooks CL (Jan 2004). "Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures". Journal of Computational Chemistry. 25 (2): 265–84. doi:10.1002/jcc.10378. PMID 14648625. S2CID 3191066.

Shoichet BK, Kuntz ID, Bodian DL (2004). "Molecular docking using shape descriptors". Journal of Computational Chemistry. 13 (3): 380–397. doi:10.1002/jcc.540130311. S2CID 42749294.

Cai W, Shao X, Maigret B (Jan 2002). "Protein-ligand recognition using spherical harmonic molecular surfaces: towards a fast and efficient filter for large virtual throughput screening". Journal of Molecular Graphics & Modelling. 20 (4): 313–28. doi:10.1016/S1093-3263(01)00134-6. PMID 11858640.

Morris RJ, Najmanovich RJ, Kahraman A, Thornton JM (May 2005). "Real spherical harmonic expansion coefficients as 3D shape descriptors for protein binding pocket and ligand comparisons". Bioinformatics. 21 (10): 2347–55. doi:10.1093/bioinformatics/bti337. PMID 15728116.

Kahraman A, Morris RJ, Laskowski RA, Thornton JM (Apr 2007). "Shape variation in protein binding pockets and their ligands". Journal of Molecular Biology. 368 (1): 283–301. doi:10.1016/j.jmb.2007.01.086. PMID 17337005.

Torres PH, Sodero AC, Jofily P, Silva-Jr FP (September 2019). "Key Topics in Molecular Docking for Drug Design". International Journal of Molecular Sciences. 20 (18): 4574. doi:10.3390/ijms20184574. PMC 6769580. PMID 31540192.

Kearsley SK, Underwood DJ, Sheridan RP, Miller MD (Oct 1994). "Flexibases: a way to enhance the use of molecular docking methods". Journal of Computer-Aided Molecular Design. 8 (5): 565–82. Bibcode:1994JCAMD...8..565K. doi:10.1007/BF00123666. PMID 7876901. S2CID 8834526.

Friesner RA, Banks JL, Murphy RB, Halgren TA, Klicic JJ, Mainz DT, Repasky MP, Knoll EH, Shelley M, Perry JK, Shaw DE, Francis P, Shenkin PS (Mar 2004). "Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy". Journal of Medicinal Chemistry. 47 (7): 1739–49. doi:10.1021/jm0306430. PMID 15027865.

Zsoldos Z, Reid D, Simon A, Sadjad SB, Johnson AP (Jul 2007). "eHiTS: a new fast, exhaustive flexible ligand docking system". Journal of Molecular Graphics & Modelling. 26 (1): 198–212. doi:10.1016/j.jmgm.2006.06.002. PMID 16860582.

Wang Q, Pang YP (September 2007). Romesberg F (ed.). "Preference of small molecules for local minimum conformations when binding to proteins". PLOS ONE. 2 (9): e820. Bibcode:2007PLoSO...2..820W. doi:10.1371/journal.pone.0000820. PMC 1959118. PMID 17786192.

Klebe G, Mietzner T (October 1994). "A fast and efficient method to generate biologically relevant conformations". Journal of Computer-Aided Molecular Design. 8 (5): 583–606. Bibcode:1994JCAMD...8..583K. doi:10.1007/BF00123667. PMID 7876902. S2CID 206768542.

Ciemny M, Kurcinski M, Kamel K, Kolinski A, Alam N, Schueler-Furman O, Kmiecik S (May 2018). "Protein-peptide docking: opportunities and challenges". Drug Discovery Today. 23 (8): 1530–1537. doi:10.1016/j.drudis.2018.05.006. PMID 29733895.

Antunes DA, Devaurs D, Kavraki LE (December 2015). "Understanding the challenges of protein flexibility in drug design" (PDF). Expert Opinion on Drug Discovery. 10 (12): 1301–13. doi:10.1517/17460441.2015.1094458. hdl:1911/88215. PMID 26414598. S2CID 6589810.

Cerqueira NM, Bras NF, Fernandes PA, Ramos MJ (January 2009). "MADAMM: a multistaged docking with an automated molecular modeling protocol". Proteins. 74 (1): 192–206. doi:10.1002/prot.22146. PMID 18618708. S2CID 36656063.

Totrov M, Abagyan R (Apr 2008). "Flexible ligand docking to multiple receptor conformations: a practical alternative". Current Opinion in Structural Biology. 18 (2): 178–84. doi:10.1016/j.sbi.2008.01.004. PMC 2396190. PMID 18302984.

Hartmann C, Antes I, Lengauer T (Feb 2009). "Docking and scoring with alternative side-chain conformations". Proteins. 74 (3): 712–26. doi:10.1002/prot.22189. PMID 18704939. S2CID 36088213.

Taylor RD, Jewsbury PJ, Essex JW (Oct 2003). "FDS: flexible ligand and receptor docking with a continuum solvent model and soft-core energy function". Journal of Computational Chemistry. 24 (13): 1637–56. CiteSeerX 10.1.1.147.1131. doi:10.1002/jcc.10295. PMID 12926007. S2CID 15814316.

Murcko MA (Dec 1995). "Computational Methods to Predict Binding Free Energy in Ligand-Receptor Complexes". Journal of Medicinal Chemistry. 38 (26): 4953–67. doi:10.1021/jm00026a001. PMID 8544170.

Arcon JP, Turjanski AG, Martí MA, Forli S (2021). Ballante F (ed.). Biased Docking for Protein-Ligand Pose Prediction. Methods in Molecular Biology. Vol. 2266. New York, NY: Springer US. pp. 39–72. doi:10.1007/978-1-0716-1209-5_3. ISBN 978-1-0716-1209-5. PMID 33759120. S2CID 232340746.

Gohlke H, Hendlich M, Klebe G (January 2000). "Knowledge-based scoring function to predict protein-ligand interactions". Journal of Molecular Biology. 295 (2): 337–356. doi:10.1006/jmbi.1999.3371. PMID 10623530.

Huang N, Shoichet BK, Irwin JJ (Nov 2006). "Benchmarking sets for molecular docking". Journal of Medicinal Chemistry. 49 (23): 6789–801. doi:10.1021/jm0608356. PMC 3383317. PMID 17154509.

Ballante F, Marshall GR (January 2016). "An Automated Strategy for Binding-Pose Selection and Docking Assessment in Structure-Based Drug Design". Journal of Chemical Information and Modeling. 56 (1): 54–72. doi:10.1021/acs.jcim.5b00603. PMID 26682916.

Bursulaya BD, Totrov M, Abagyan R, Brooks CL (November 2003). "Comparative study of several algorithms for flexible ligand docking". Journal of Computer-Aided Molecular Design. 17 (11): 755–763. Bibcode:2003JCAMD..17..755B. doi:10.1023/B:JCAM.0000017496.76572.6f. PMID 15072435. S2CID 12569345.

Ballante F (2018). "Protein-Ligand Docking in Drug Design: Performance Assessment and Binding-Pose Selection". Rational Drug Design. Methods in Molecular Biology. Vol. 1824. pp. 67–88. doi:10.1007/978-1-4939-8630-9_5. ISBN 978-1-4939-8629-3. PMID 30039402.

Irwin JJ (2008-02-14). "Community benchmarks for virtual screening". Journal of Computer-Aided Molecular Design. 22 (3–4): 193–199. Bibcode:2008JCAMD..22..193I. doi:10.1007/s10822-008-9189-4. PMID 18273555. S2CID 26260725.

Ballante F, Kooistra AJ, Kampen S, de Graaf C, Carlsson J (October 2021). "Structure-Based Virtual Screening for Ligands of G Protein-Coupled Receptors: What Can Molecular Docking Do for You?". Pharmacological Reviews. 73 (4): 527–565. doi:10.1124/pharmrev.120.000246. PMID 34907092. S2CID 245163594.

Hartshorn MJ, Verdonk ML, Chessari G, Brewerton SC, Mooij WT, Mortenson PN, Murray CW (Feb 2007). "Diverse, high-quality test set for the validation of protein-ligand docking performance". Journal of Medicinal Chemistry. 50 (4): 726–41. doi:10.1021/jm061277y. PMID 17300160.

Chachulski L, Windshügel B (Dec 2020). "LEADS-FRAG: A Benchmark Data Set for Assessment of Fragment Docking Performance". Journal of Chemical Information and Modeling. 60 (12): 6544–6554. doi:10.1021/acs.jcim.0c00693. PMID 33289563.

Hauser AS, Windshügel B (Dec 2015). "A Benchmark Data Set for Assessment of Peptide Docking Performance". Journal of Chemical Information and Modeling. 56 (1): 188–200. doi:10.1021/acs.jcim.5b00234. PMID 26651532.

Suresh PS, Kumar A, Kumar R, Singh VP (Jan 2008). "An in silico [correction of insilico] approach to bioremediation: laccase as a case study". Journal of Molecular Graphics & Modelling. 26 (5): 845–9. doi:10.1016/j.jmgm.2007.05.005. PMID 17606396.

Basharat Z, Yasmin A, Bibi M (2020). "Implications of Molecular Docking Assay for Bioremediation". Data Analytics in Medicine: Concepts, Methodologies, Tools, and Applications. Advances in Environmental Engineering and Green Technologies. IGI Global. pp. 1556–1577. doi:10.4018/978-1-5225-2325-3.ch002. ISBN 978-1799812043. S2CID 63136337.

harvard.edu

ui.adsabs.harvard.edu

Jorgensen WL (Nov 1991). "Rusting of the lock and key model for protein-ligand binding". Science. 254 (5034): 954–5. Bibcode:1991Sci...254..954J. doi:10.1126/science.1719636. PMID 1719636.

nih.gov

pubmed.ncbi.nlm.nih.gov

Lengauer T, Rarey M (Jun 1996). "Computational methods for biomolecular docking". Current Opinion in Structural Biology. 6 (3): 402–6. doi:10.1016/S0959-440X(96)80061-3. PMID 8804827.

Jorgensen WL (Nov 1991). "Rusting of the lock and key model for protein-ligand binding". Science. 254 (5034): 954–5. Bibcode:1991Sci...254..954J. doi:10.1126/science.1719636. PMID 1719636.

Hartmann C, Antes I, Lengauer T (Feb 2009). "Docking and scoring with alternative side-chain conformations". Proteins. 74 (3): 712–26. doi:10.1002/prot.22189. PMID 18704939. S2CID 36088213.

Murcko MA (Dec 1995). "Computational Methods to Predict Binding Free Energy in Ligand-Receptor Complexes". Journal of Medicinal Chemistry. 38 (26): 4953–67. doi:10.1021/jm00026a001. PMID 8544170.

Huang N, Shoichet BK, Irwin JJ (Nov 2006). "Benchmarking sets for molecular docking". Journal of Medicinal Chemistry. 49 (23): 6789–801. doi:10.1021/jm0608356. PMC 3383317. PMID 17154509.

ncbi.nlm.nih.gov

psu.edu

citeseerx.ist.psu.edu

semanticscholar.org

api.semanticscholar.org

Meng EC, Shoichet BK, Kuntz ID (1992). "Automated docking with grid-based energy evaluation". Journal of Computational Chemistry. 13 (4): 505–524. doi:10.1002/jcc.540130412. S2CID 97778840.

Shoichet BK, Kuntz ID, Bodian DL (2004). "Molecular docking using shape descriptors". Journal of Computational Chemistry. 13 (3): 380–397. doi:10.1002/jcc.540130311. S2CID 42749294.

Hartmann C, Antes I, Lengauer T (Feb 2009). "Docking and scoring with alternative side-chain conformations". Proteins. 74 (3): 712–26. doi:10.1002/prot.22189. PMID 18704939. S2CID 36088213.

Docking (molecular) (English Wikipedia)

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