Evaluation of the Wilma-SIE Virtual Screening Method in Community Structure-Activity Resource 2013 and 2014 Blind Challenges

Journal of Chemical Information and Modeling

Volumn 56, Issue 6, 2016, Pages 955-964

  Hogues, Hervé ^a   Sulea, Traian ^a   Purisima, Enrico O ^a  

^a NATIONAL RESEARCH COUNCIL CANADA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; HYDROGEN BONDS;

COMMUNITY STRUCTURES; INTERACTION ENERGIES; METHYLTRANSFERASES; MOLECULAR TARGETS; MULTIPLE TARGETS; PROTONATION STATE; STRUCTURAL DOMAINS; VIRTUAL SCREENING;

LIGANDS;

LIGAND; PROTEIN; PROTEIN BINDING;

CHEMISTRY; EVALUATION STUDY; METABOLISM; MOLECULAR DOCKING; PRECLINICAL STUDY; PROCEDURES; PROTEIN CONFORMATION; STRUCTURE ACTIVITY RELATION;

DRUG EVALUATION, PRECLINICAL; LIGANDS; MOLECULAR DOCKING SIMULATION; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEINS; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 84976351167     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/acs.jcim.5b00278     Document Type: Article

References (34)

1. McInnes, C. Virtual Screening Strategies in Drug Discovery Curr. Opin. Chem. Biol. 2007, 11, 494-502 10.1016/j.cbpa.2007.08.033
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, 935-949 10.1038/nrd1549
3. Sliwoski, G.; Kothiwale, S.; Meiler, J.; Lowe, E. W., Jr. Computational Methods in Drug Discovery Pharmacol. Rev. 2013, 66, 334-395 10.1124/pr.112.007336
4. Sulea, T.; Hogues, H.; Purisima, E. O. Exhaustive Search and Solvated Interaction Energy (SIE) for Virtual Screening and Affinity Prediction J. Comput.-Aided Mol. Des. 2012, 26, 617-633 10.1007/s10822-011-9529-7
5. Hogues, H.; Sulea, T.; Purisima, E. O. Exhaustive Docking and Solvated Interaction Energy Scoring: Lessons Learned from the SAMPL4 Challenge J. Comput.-Aided Mol. Des. 2014, 28, 417-427 10.1007/s10822-014-9715-5
6. Naim, M.; Bhat, S.; Rankin, K. N.; Dennis, S.; Chowdhury, S. F.; Siddiqi, I.; Drabik, P.; Sulea, T.; Bayly, C. I.; Jakalian, A.; Purisima, E. O. Solvated Interaction Energy (SIE) for Scoring Protein-Ligand Binding Affinities. 1. Exploring the Parameter Space J. Chem. Inf. Model. 2007, 47, 122-133 10.1021/ci600406v
7. Cui, Q.; Sulea, T.; Schrag, J. D.; Munger, C.; Hung, M. N.; Naim, M.; Cygler, M.; Purisima, E. O. Molecular Dynamics - Solvated Interaction Energy Studies of Protein-Protein Interactions: The Mp1-P14 Scaffolding Complex J. Mol. Biol. 2008, 379, 787-802 10.1016/j.jmb.2008.04.035
8. Sulea, T.; Purisima, E. O. The Solvated Interaction Energy Method for Scoring Binding Affinities Methods Mol. Biol. 2012, 819, 295-303 10.1007/978-1-61779-465-0-19
9. Kollman, P. A.; Massova, I.; Reyes, C.; Kuhn, B.; Huo, S.; Chong, L.; Lee, M.; Lee, T.; Duan, Y.; Wang, W.; Donini, O.; Cieplak, P.; Srinivasan, J.; Case, D. A.; Cheatham, T. E. Calculating Structures and Free Energies of Complex Molecules: Combining Molecular Mechanics and Continuum Models Acc. Chem. Res. 2000, 33, 889-897 10.1021/ar000033j
10. Brown, S. P.; Muchmore, S. W. Large-Scale Application of High-Throughput Molecular Mechanics with Poisson-Boltzmann Surface Area for Routine Physics-Based Scoring of Protein-Ligand Complexes J. Med. Chem. 2009, 52, 3159-3165 10.1021/jm801444x
11. Gohlke, H.; Kiel, C.; Case, D. A. Converging Free Energy Estimates: MM-PB(GB)SA Studies on the Protein-Protein Complex Ras-Raf J. Comput. Chem. 2004, 25, 238-250 10.1002/jcc.10379
12. Sulea, T.; Cui, Q.; Purisima, E. O. Solvated Interaction Energy (SIE) for Scoring Protein-Ligand Binding Affinities. 2. Benchmark in the CSAR-2010 Scoring Exercise J. Chem. Inf. Model. 2011, 51, 2066-2081 10.1021/ci2000242
13. Skillman, A. SAMPL1 at First Glance. CUP IX meeting, Santa Fe, NM, March 19, 2008.
14. Corbeil, C. R.; Sulea, T.; Purisima, E. O. Rapid Prediction of Solvation Free Energy. 2. The First-Shell Hydration (FiSH) Continuum Model J. Chem. Theory Comput. 2010, 6, 1622-1637 10.1021/ct9006037
15. Dunbar, J. B., Jr.; Smith, R. D.; Yang, C. Y.; Ung, P. M.; Lexa, K. W.; Khazanov, N. A.; Stuckey, J. A.; Wang, S.; Carlson, H. A. CSAR Benchmark Exercise of 2010: Selection of the Protein-Ligand Complexes J. Chem. Inf. Model. 2011, 51, 2036-2046 10.1021/ci200082t
16. Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules J. Am. Chem. Soc. 1995, 117, 5179-5197 10.1021/ja00124a002
17. Case, D. A.; Cheatham, T. E.; Darden, T.; Gohlke, H.; Luo, R.; Merz, K. M.; Onufriev, A.; Simmerling, C.; Wang, B.; Woods, R. J. The Amber Biomolecular Simulation Programs J. Comput. Chem. 2005, 26, 1668-1688 10.1002/jcc.20290
18. Wang, J.; Wolf, R. M.; Caldwell, J. W.; Kollman, P. A.; Case, D. A. Development and Testing of a General Amber Force Field J. Comput. Chem. 2004, 25, 1157-1174 10.1002/jcc.20035
19. Purisima, E. O. Fast Summation Boundary Element Method for Calculating Solvation Free Energies of Macromolecules J. Comput. Chem. 1998, 19, 1494-1504 10.1002/(SICI)1096-987X(199810)19:13<1494::AID-JCC6>3.3.CO;2-A
20. Purisima, E. O.; Nilar, S. H. A Simple yet Accurate Boundary Element Method for Continuum Dielectric Calculations J. Comput. Chem. 1995, 16, 681-689 10.1002/jcc.540160604
21. Chan, S. L.; Purisima, E. O. Molecular Surface Generation Using Marching Tetrahedra J. Comput. Chem. 1998, 19, 1268-1277 10.1002/(SICI)1096-987X(199808)19:11<1268::AID-JCC6>3.0.CO;2-I
22. Chan, S. L.; Purisima, E. O. A New Tetrahedral Tesselation Scheme for Isosurface Generation Comput. Graph. 1998, 22, 83-90 10.1016/S0097-8493(97)00085-X
23. Bhat, S.; Purisima, E. O. Molecular Surface Generation Using a Variable-Radius Solvent Probe Proteins: Struct., Funct., Genet. 2006, 62, 244-261 10.1002/prot.20682
24. Jakalian, A.; Bush, B. L.; Jack, D. B.; Bayly, C. I. Fast, Efficient Generation of High-Quality Atomic Charges. AM1-BCC Model: I. Method J. Comput. Chem. 2000, 21, 132-146 10.1002/(SICI)1096-987X(20000130)21:2<132::AID-JCC5>3.0.CO;2-P
25. Jakalian, A.; Jack, D. B.; Bayly, C. I. Fast, Efficient Generation of High-Quality Atomic Charges. AM1-BCC Model: II. Parameterization and Validation J. Comput. Chem. 2002, 23, 1623-1641 10.1002/jcc.10128
26. Chang, C. E.; Gilson, M. K. Free Energy, Entropy, and Induced Fit in Host-Guest Recognition: Calculations with the Second-Generation Mining Minima Algorithm J. Am. Chem. Soc. 2004, 126, 13156-13164 10.1021/ja047115d
27. Chen, W.; Chang, C. E.; Gilson, M. K. Calculation of Cyclodextrin Binding Affinities: Energy, Entropy, and Implications for Drug Design Biophys. J. 2004, 87, 3035-3049 10.1529/biophysj.104.049494
28. Purisima, E.; Corbeil, C.; Sulea, T. Rapid Prediction of Solvation Free Energy. 3. Application to the SAMPL2 Challenge J. Comput.-Aided Mol. Des. 2010, 24, 373-383 10.1007/s10822-010-9341-9
29. Halgren, T. A. Merk Molecular Force Field. I. Basis, Form, Scope, Parametrization, and Performance of MMMFF94 J. Comput. Chem. 1996, 17, 490-519 10.1002/(SICI)1096-987X(199604)17:5/6<490::AID-JCC1>3.0.CO;2-P
30. Halgren, T. A. MMFF VII. Characterization of MMFF94, MMFF94s, and Other Widely Available Force Fields for Conformational Energies and for Intermolecular-Interaction Energies and Geometries J. Comput. Chem. 1999, 20, 730-748 10.1002/(SICI)1096-987X(199905)20:7<730::AID-JCC8>3.3.CO;2-K
31. Greenwood, J. R.; Calkins, D.; Sullivan, A. P.; Shelley, J. C. Towards the Comprehensive, Rapid, and Accurate Prediction of the Favorable Tautomeric States of Drug-Like Molecules in Aqueous Solution J. Comput.-Aided Mol. Des. 2010, 24, 591-604 10.1007/s10822-010-9349-1
32. Shelley, J. C.; Cholleti, A.; Frye, L. L.; Greenwood, J. R.; Timlin, M. R.; Uchimaya, M. Epik: A Software Program for pK(a) Prediction and Protonation State Generation for Drug-Like Molecules J. Comput.-Aided Mol. Des. 2007, 21, 681-691 10.1007/s10822-007-9133-z
33. Damm, K. L.; Carlson, H. A. Gaussian-Weighted RMSD Superposition of Proteins: A Structural Comparison for Flexible Proteins and Predicted Protein Structures Biophys. J. 2006, 90, 4558-4573 10.1529/biophysj.105.066654
34. Smith, R. D.; Dunbar, J. B., Jr.; Ung, P. M.; Esposito, E. X.; Yang, C. Y.; Wang, S.; Carlson, H. A. CSAR Benchmark Exercise of 2010: Combined Evaluation across All Submitted Scoring Functions J. Chem. Inf. Model. 2011, 51, 2115-2131 10.1021/ci200269q