A Hybrid Knowledge-Based and Empirical Scoring Function for Protein-Ligand Interaction: SMoG2016

Journal of Chemical Information and Modeling

Volumn 57, Issue 3, 2017, Pages 584-593

  Debroise, Théau ^a   Shakhnovich, Eugene I ^a   Chéron, Nicolas ^a,b  

^a HARVARD UNIVERSITY   (United States)

^b ECOLE NORMALE SUPÉRIEURE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING ENERGY; CORRELATION METHODS; FREE ENERGY; LIGANDS; PROTEINS;

BINDING FREE ENERGY; EMPIRICAL FUNCTIONS; OPEN SOURCE PROJECTS; PAIRWISE INTERACTION; PEARSON CORRELATION COEFFICIENTS; PROTEIN-LIGAND INTERACTIONS; SCORING FUNCTIONS; STANDARD DEVIATION;

KNOWLEDGE BASED SYSTEMS;

LIGAND; PROTEIN; PROTEIN BINDING;

CHEMISTRY; ENTROPY; KNOWLEDGE BASE; METABOLISM; MOLECULAR MODEL; PROBABILITY; PROTEIN CONFORMATION; PROTEIN DATABASE;

DATABASES, PROTEIN; ENTROPY; KNOWLEDGE BASES; LIGANDS; MODELS, MOLECULAR; PROBABILITY; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEINS;

EID: 85025107228     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/acs.jcim.6b00610     Document Type: Article

References (46)

1. Chéron, N.; Jasty, N.; Shakhnovich, E. I. OpenGrowth: An Automated and Rational Algorithm for Finding New Protein Inhibitors J. Med. Chem. 2016, 59 (9) 4171-4188 10.1021/acs.jmedchem.5b00886
2. Kitchen, D. B.; Decornez, H.; Furr, J. R.; Bajorath, J. Docking and Scoring in Virtual Screening for Drug Discovery: Methods and Applications Nat. Rev. Drug Discovery 2004, 3 (11) 935-949 10.1038/nrd1549
3. Liu, J.; Wang, R. Classification of Current Scoring Functions J. Chem. Inf. Model. 2015, 55 (3) 475-482 10.1021/ci500731a
4. Jones, G.; Willett, P.; Glen, R. C.; Leach, A. R.; Taylor, R. Development and Validation of a Genetic Algorithm for Flexible Docking J. Mol. Biol. 1997, 267 (3) 727-748 10.1006/jmbi.1996.0897
5. Verdonk, M. L.; Cole, J. C.; Hartshorn, M. J.; Murray, C. W.; Taylor, R. D. Improved Protein-ligand Docking Using GOLD Proteins: Struct., Funct., Genet. 2003, 52 (4) 609-623 10.1002/prot.10465
6. Eldridge, M. D.; Murray, C. W.; Auton, T. R.; Paolini, G. V.; Mee, R. P. Empirical Scoring Functions: I. The Development of a Fast Empirical Scoring Function to Estimate the Binding Affinity of Ligands in Receptor Complexes J. Comput.-Aided Mol. Des. 1997, 11 (5) 425-445 10.1023/A:1007996124545
7. DeWitte, R. S.; Shakhnovich, E. I. SMoG: De Novo Design Method Based on Simple, Fast, and Accurate Free Energy Estimates. 1. Methodology and Supporting Evidence J. Am. Chem. Soc. 1996, 118 (47) 11733-11744 10.1021/ja960751u
8. Ishchenko, A. V.; Shakhnovich, E. I. SMall Molecule Growth 2001 (SMoG2001): An Improved Knowledge-Based Scoring Function for Protein-Ligand Interactions J. Med. Chem. 2002, 45 (13) 2770-2780 10.1021/jm0105833
9. Li, Y.; Han, L.; Liu, Z.; Wang, R. Comparative Assessment of Scoring Functions on an Updated Benchmark: 2. Evaluation Methods and General Results J. Chem. Inf. Model. 2014, 54 (6) 1717-1736 10.1021/ci500081m
10. Li, Y.; Liu, Z.; Li, J.; Han, L.; Liu, J.; Zhao, Z.; Wang, R. Comparative Assessment of Scoring Functions on an Updated Benchmark: 1. Compilation of the Test Set J. Chem. Inf. Model. 2014, 54 (6) 1700-1716 10.1021/ci500080q
11. O'Boyle, N.; Banck, M.; James, C.; Morley, C.; Vandermeersch, T.; Hutchison, G. Open Babel: An Open Chemical Toolbox J. Cheminf. 2011, 3 (1) 33 10.1186/1758-2946-3-33
12. Tanimoto, T. An Elementary Mathematical Theory of Classification and Prediction; Internal IBM Technical Report; IBM: New York, 1958.
13. Larkin, M. A.; Blackshields, G.; Brown, N. P.; Chenna, R.; McGettigan, P. A.; McWilliam, H.; Valentin, F.; Wallace, I. M.; Wilm, A.; Lopez, R.; Thompson, J. D.; Gibson, T. J.; Higgins, D. G. Clustal W and Clustal X version 2.0 Bioinformatics 2007, 23 (21) 2947-2948 10.1093/bioinformatics/btm404
14. Chen, W. W.; Shakhnovich, E. I. Lessons from the Design of a Novel Atomic Potential for Protein Folding Protein Sci. 2005, 14 (7) 1741-1752 10.1110/ps.051440705
15. Neudert, G.; Klebe, G. DSX: A Knowledge-Based Scoring Function for the Assessment of Protein-Ligand Complexes J. Chem. Inf. Model. 2011, 51 (10) 2731-2745 10.1021/ci200274q
16. Tanchuk, V. Y.; Tanin, V. O.; Vovk, A. I.; Poda, G. A New, Improved Hybrid Scoring Function for Molecular Docking and Scoring Based on AutoDock and AutoDock Vina Chem. Biol. Drug Des. 2016, 87 (4) 618-625 10.1111/cbdd.12697
17. Duan, Y.; Wu, C.; Chowdhury, S.; Lee, M. C.; Xiong, G.; Zhang, W.; Yang, R.; Cieplak, P.; Luo, R.; Lee, T.; Caldwell, J.; Wang, J.; Kollman, P. A Point-Charge Force Field for Molecular Mechanics Simulations of Proteins Based on Condensed-Phase Quantum Mechanical Calculations J. Comput. Chem. 2003, 24 (16) 1999-2012 10.1002/jcc.10349
18. King, D. E. Dlib-Ml: A Machine Learning Toolkit J. Mach. Learn. Res. 2009, 10, 1755-1758
19. Dunbrack, R. L.; Cohen, F. E. Bayesian Statistical Analysis of Protein Side-Chain Rotamer Preferences Protein Sci. 1997, 6 (8) 1661-1681 10.1002/pro.5560060807
20. Mitternacht, S. FreeSASA: An Open Source C Library for Solvent Accessible Surface Area Calculations F1000Research 2016, 5, 189 10.12688/f1000research.7931.1
21. Wang, R.; Lai, L.; Wang, S. Further Development and Validation of Empirical Scoring Functions for Structure-Based Binding Affinity Prediction J. Comput.-Aided Mol. Des. 2002, 16 (1) 11-26 10.1023/A:1016357811882
22. Lee, B.; Richards, F. M. The Interpretation of Protein Structures: Estimation of Static Accessibility J. Mol. Biol. 1971, 55 (3) 379-IN4 10.1016/0022-2836(71)90324-X
23. Andrews, P. R.; Craik, D. J.; Martin, J. L. Functional Group Contributions to Drug-Receptor Interactions J. Med. Chem. 1984, 27 (12) 1648-1657 10.1021/jm00378a021
24. Huey, R.; Morris, G. M.; Olson, A. J.; Goodsell, D. S. A Semiempirical Free Energy Force Field with Charge-Based Desolvation J. Comput. Chem. 2007, 28 (6) 1145-1152 10.1002/jcc.20634
25. McQuarrie, D. A.; Simon, J. D. Molecular Thermodynamics; University Science Books: Sausalito, CA, 1999.
26. Jain, A. N. Scoring Noncovalent Protein-Ligand Interactions: A Continuous Differentiable Function Tuned to Compute Binding Affinities J. Comput.-Aided Mol. Des. 1996, 10 (5) 427-440 10.1007/BF00124474
27. Zhou, H.-X.; Gilson, M. K. Theory of Free Energy and Entropy in Noncovalent Binding Chem. Rev. 2009, 109 (9) 4092-4107 10.1021/cr800551w
28. Li, G.-B.; Yang, L.-L.; Wang, W.-J.; Li, L.-L.; Yang, S.-Y. ID-Score: A New Empirical Scoring Function Based on a Comprehensive Set of Descriptors Related to Protein-Ligand Interactions J. Chem. Inf. Model. 2013, 53 (3) 592-600 10.1021/ci300493w
29. Wang, R.; Lai, L.; Wang, S. Further Development and Validation of Empirical Scoring Functions for Structure-Based Binding Affinity Prediction J. Comput.-Aided Mol. Des. 2002, 16 (1) 11-26 10.1023/A:1016357811882
30. Korb, O.; Stützle, T.; Exner, T. E. Empirical Scoring Functions for Advanced Protein-Ligand Docking with PLANTS J. Chem. Inf. Model. 2009, 49 (1) 84-96 10.1021/ci800298z
31. Verkhivker, G.; Appelt, K.; Freer, S. T.; Villafranca, J. E. Empirical Free Energy Calculations of Ligand-Protein Crystallographic Complexes. I. Knowledge-Based Ligand-Protein Interaction Potentials Applied to the Prediction of Human Immunodeficiency Virus 1 Protease Binding Affinity Protein Eng., Des. Sel. 1995, 8 (7) 677-691 10.1093/protein/8.7.677
32. Verkhivker, G. M.; Bouzida, D.; Gehlhaar, D. K.; Rejto, P. A.; Arthurs, S.; Colson, A. B.; Freer, S. T.; Larson, V.; Luty, B. A.; Marrone, T.; Rose, P. W. Deciphering Common Failures in Molecular Docking of Ligand-Protein Complexes J. Comput.-Aided Mol. Des. 2000, 14 (8) 731-751 10.1023/A:1008158231558
33. Mooij, W. T. M.; Verdonk, M. L. General and Targeted Statistical Potentials for Protein-Ligand Interactions Proteins: Struct., Funct., Genet. 2005, 61 (2) 272-287 10.1002/prot.20588
34. Ewing, T. J. A.; Makino, S.; Skillman, A. G.; Kuntz, I. D. DOCK 4.0: Search Strategies for Automated Molecular Docking of Flexible Molecule Databases J. Comput.-Aided Mol. Des. 2001, 15 (5) 411-428 10.1023/A:1011115820450
35. Böhm, H.-J. The Development of a Simple Empirical Scoring Function to Estimate the Binding Constant for a Protein-Ligand Complex of Known Three-Dimensional Structure J. Comput.-Aided Mol. Des. 1994, 8 (3) 243-256 10.1007/BF00126743
36. Böhm, H.-J. Prediction of Binding Constants of Protein Ligands: A Fast Method for the Prioritization of Hits Obtained from de Novo Design or 3D Database Search Programs J. Comput.-Aided Mol. Des. 1998, 12 (4) 309-309 10.1023/A:1007999920146
37. Krammer, A.; Kirchhoff, P. D.; Jiang, X.; Venkatachalam, C. M.; Waldman, M. LigScore: A Novel Scoring Function for Predicting Binding Affinities J. Mol. Graphics Modell. 2005, 23 (5) 395-407 10.1016/j.jmgm.2004.11.007
38. Friesner, R. A.; Banks, J. L.; Murphy, R. B.; Halgren, T. A.; Klicic, J. J.; Mainz, D. T.; Repasky, M. P.; Knoll, E. H.; Shelley, M.; Perry, J. K.; Shaw, D. E.; Francis, P.; Shenkin, P. S. Glide: A New Approach for Rapid, Accurate Docking and Scoring. 1. Method and Assessment of Docking Accuracy J. Med. Chem. 2004, 47 (7) 1739-1749 10.1021/jm0306430
39. Halgren, T. A.; Murphy, R. B.; Friesner, R. A.; Beard, H. S.; Frye, L. L.; Pollard, W. T.; Banks, J. L. Glide: A New Approach for Rapid, Accurate Docking and Scoring. 2. Enrichment Factors in Database Screening J. Med. Chem. 2004, 47 (7) 1750-1759 10.1021/jm030644s
40. Muegge, I.; Martin, Y. C. A General and Fast Scoring Function for Protein-Ligand Interactions: A Simplified Potential Approach J. Med. Chem. 1999, 42 (5) 791-804 10.1021/jm980536j
41. Muegge, I. Effect of Ligand Volume Correction on PMF Scoring J. Comput. Chem. 2001, 22 (4) 418-425 10.1002/1096-987X(200103)22:4<418::AID-JCC1012>3.0.CO;2-3
42. Muegge, I. A Knowledge-Based Scoring Function for Protein-Ligand Interactions: Probing the Reference State. In Virtual Screening: An Alternative or Complement to High Throughput Screening?; Klebe, G., Ed.; Kluwer Academic Publishers: New York, 2002; pp 99-114.
43. Muegge, I. PMF Scoring Revisited J. Med. Chem. 2006, 49 (20) 5895-5902 10.1021/jm050038s
44. Friesner, R. A.; Murphy, R. B.; Repasky, M. P.; Frye, L. L.; Greenwood, J. R.; Halgren, T. A.; Sanschagrin, P. C.; Mainz, D. T. Extra Precision Glide: Docking and Scoring Incorporating a Model of Hydrophobic Enclosure for Protein-Ligand Complexes J. Med. Chem. 2006, 49 (21) 6177-6196 10.1021/jm051256o
45. Jencks, W. P. Binding Energy, Specificity, and Enzymic Catalysis: The Circe Effect Adv. Enzymol. Relat. Areas Mol. Biol. 1975, 43, 219-410
46. Jencks, W. P. Reaction Mechanisms, Catalysis, and Movement Protein Sci. 1994, 3 (12) 2459-2464 10.1002/pro.5560031232