Empirical Scoring Functions for Affinity Prediction of Protein-ligand Complexes

Molecular Informatics

Volumn 35, Issue 11-12, 2016, Pages 541-548

  Pason, Lukas P ^a   Sotriffer, Christoph A ^a  

^a UNIVERSITY OF WÜRZBURG   (Germany)

Author keywords

binding free energy; descriptors; docking; machine learning; structure based drug design

Indexed keywords

ARTIFICIAL INTELLIGENCE; BINDING ENERGY; COMPLEXATION; FREE ENERGY; LEARNING SYSTEMS; PROTEINS; STRUCTURAL DESIGN;

BINDING FREE ENERGY; COMPUTER AIDED DRUG DESIGN; DESCRIPTORS; DOCKING; MACHINE-LEARNING; MATCHINGS; PROTEIN-LIGAND COMPLEXES; SCORING FUNCTIONS; SIMPLE++; STRUCTURE BASED DRUG DESIGNS;

LIGANDS;

LIGAND; PROTEIN; PROTEIN LIGAND COMPLEX; UNCLASSIFIED DRUG; PROTEIN BINDING;

ARTICLE; ENERGY; FILTRATION; LINEAR REGRESSION ANALYSIS; MACHINE LEARNING; MOLECULAR DOCKING; PREDICTION; PRIORITY JOURNAL; PROTEIN INTERACTION; SCREENING; SIMULATION; BINDING SITE; BIOLOGY; CHEMISTRY; PHYSIOLOGY; PROCEDURES; REGRESSION ANALYSIS; STATISTICAL MODEL;

BINDING SITES; COMPUTATIONAL BIOLOGY; LIGANDS; LINEAR MODELS; MACHINE LEARNING; MOLECULAR DOCKING SIMULATION; PROTEIN BINDING; PROTEINS; REGRESSION ANALYSIS;

EID: 84978269171     PISSN: 18681743     EISSN: 18681751     Source Type: Journal    
DOI: 10.1002/minf.201600048     Document Type: Article

References (47)

1. H. Gohlke, G. Klebe, Angew. Chem. Int. Ed. 2002, 41, 2644–2676;
2. C. Sotriffer, H. Matter, in Virtual Screening. Principles, Challenges, and Practical Guidelines, Vol. 48 (Ed.: C. Sotriffer), Wiley-VCH, Weinheim, 2011, pp. 177–221.
3. M. K. Gilson, J. A. Given, B. L. Bush, J. A. McCammon, Biophys. J. 1997, 72, 1047–1069.
4. T. B. Steinbrecher, M. Dahlgren, D. Cappel, T. Lin, L. Wang, G. Krilov, R. Abel, R. Friesner, W. Sherman, J. Chem. Inf. Model. 2015, 55, 2411–2420.
5. S. Y. Huang, S. Z. Grinter, X. Zou, Phys. Chem. Chem. Phys. 2010, 12, 12899–12908;
6. N. Moitessier, P. Englebienne, D. Lee, J. Lawandi, C. R. Corbeil, Br. J. Pharmacol. 2008, 153 Suppl. 1, S7–26;
7. C. Sotriffer, in Protein-Ligand Interactions, Vol. 53 (Ed.: H. Gohlke), Wiley-VCH, Weinheim, 2012, pp. 237–263.
8. C. A. Sotriffer, M. Stahl, H. J. Boehm, G. Klebe, in Burger′s Medicinal Chemistry and Drug Discovery, 6th edition, Vol. 1 (Ed.: D. J. Abraham), Wiley, New York, 2003, pp. 281–333.
9. J. Liu, R. Wang, J. Chem. Inf. Model. 2015, 55, 475–482.
10. Q. U. Ain, A. Aleksandrova, F. D. Roessler, P. J. Ballester, Wires Comput. Mol. Sci. 2015, 5, 405–424.
11. S. L. Kinnings, N. Liu, P. J. Tonge, R. M. Jackson, L. Xie, P. E. Bourne, J. Chem. Inf. Model. 2011, 51, 408–419;
12. M. H. Seifert, Drug Discov. Today 2009, 14, 562–569.
13. L. Hu, M. L. Benson, R. D. Smith, M. G. Lerner, H. A. Carlson, Proteins 2005, 60, 333–340.
14. R. Wang, X. Fang, Y. Lu, S. Wang, J. Med. Chem. 2004, 47, 2977–2980;
15. R. Wang, X. Fang, Y. Lu, C. Y. Yang, S. Wang, J. Med. Chem. 2005, 48, 4111–4119.
16. J. C. Cole, O. Korb, T. S. G. Olsson, J. Liebeschuetz, in Virtual Screening. Principles, Challenges, and Practical Guidelines, Vol. 48 (Ed.: C. Sotriffer), Wiley-VCH, Weinheim, 2011, pp. 87–114.
17. C. Kramer, T. Kalliokoski, P. Gedeck, A. Vulpetti, J. Med. Chem. 2012, 55, 5165–5173.
18. C. A. Sotriffer, P. Sanschagrin, H. Matter, G. Klebe, Proteins 2008, 73, 395–419.
19. P. J. Ballester, J. B. Mitchell, Bioinformatics 2010, 26, 1169–1175;
20. P. J. Ballester, A. Schreyer, T. L. Blundell, J. Chem. Inf. Model. 2014, 54, 944–955.
21. J. Gabel, J. Desaphy, D. Rognan, J. Chem. Inf. Model. 2014, 54, 2807–2815.
22. H. J. Boehm, J. Comput. Aided Mol. Des. 1994, 8, 243–256.
23. M. D. Eldridge, C. W. Murray, T. R. Auton, G. V. Paolini, R. P. Mee, J. Comput. Aided Mol. Des. 1997, 11, 425–445.
24. H. J. Boehm, J. Comput. Aided Mol. Des. 1998, 12, 309–323.
25. R. Wang, L. Lai, S. Wang, J. Comput. Aided Mol. Des. 2002, 16, 11–26.
26. S. Das, M. P. Krein, C. M. Breneman, J. Chem. Inf. Model. 2010, 50, 298–308.
27. J. D. Durrant, J. A. McCammon, J. Chem. Inf. Model. 2010, 50, 1865–1871.
28. D. Zilian, C. A. Sotriffer, J. Chem. Inf. Model. 2013, 53, 1923–1933.
29. T. Cheng, X. Li, Y. Li, Z. Liu, R. Wang, J. Chem. Inf. Model. 2009, 49, 1079–1093;
30. P. Englebienne, N. Moitessier, J. Chem. Inf. Model. 2009, 49, 1568–1580;
31. I. J. Enyedy, W. J. Egan, J. Comput. Aided Mol. Des. 2008, 22, 161–168;
32. R. Kim, J. Skolnick, J. Comput. Chem. 2008, 29, 1316–1331.
33. Y. Li, Z. Liu, J. Li, L. Han, J. Liu, Z. Zhao, R. Wang, J. Chem. Inf. Model. 2014, 54, 1700–1716.
34. J. B. Dunbar, Jr., R. D. Smith, C. Y. Yang, P. M. Ung, K. W. Lexa, N. A. Khazanov, J. A. Stuckey, S. Wang, H. A. Carlson, J. Chem. Inf. Model. 2011, 51, 2036–2046.
35. Y. Li, L. Han, Z. Liu, R. Wang, J. Chem. Inf. Model. 2014, 54, 1717–1736;
36. R. D. Smith, J. B. Dunbar, Jr., P. M. Ung, E. X. Esposito, C. Y. Yang, S. Wang, H. A. Carlson, J. Chem. Inf. Model. 2011, 51, 2115–2131.
37. B. Ari, H. A. Guvenir, Knowl-Based Syst 2002, 15, 169–175.
38. C. Bouveyron, S. Girard, C. Schmid, Comput. Stat. Data. An. 2007, 52, 502–519.
39. L. Berge, C. Bouveyron, S. Girard, J. Stat. Softw. 2012, 46, 1–29.
40. L. Torgo, J. P. Da Costa, Mach. Learn. 2003, 50, 303–319.
41. T. M. Cover, P. E. Hart, Ieee T Inform Theory 1967, 13, 21.
42. A. M. Davis, S. J. Teague, G. J. Kleywegt, Angew. Chem. Int. Ed. Engl. 2003, 42, 2718–2736;
43. M. T. Stubbs, S. Reyda, F. Dullweber, M. Moller, G. Klebe, D. Dorsch, W. W. Mederski, H. Wurziger, Chembiochem. 2002, 3, 246–249.
44. P. Czodrowski, I. Dramburg, C. A. Sotriffer, G. Klebe, Proteins 2006, 65, 424–437.
45. E. T. Boder, K. S. Midelfort, K. D. Wittrup, Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 10701–10705.
46. J. B. Dunbar, Jr., R. D. Smith, C. Y. Yang, P. M. U. Ung, K. W. Lexa, N. A. Khazanov, J. A. Stuckey, S. M. Wang, H. A. Carlson, J. Chem. Inf. Model. 2011, 51, 2146–2146.
47. W. Chen, M. K. Gilson, S. P. Webb, M. J. Potter, J. Chem. Theory Comput. 2010, 6, 3540–3557.