CSAR Benchmark of Flexible MedusaDock in Affinity Prediction and Nativelike Binding Pose Selection

Journal of Chemical Information and Modeling

Volumn 56, Issue 6, 2016, Pages 1042-1052

  Nedumpully Govindan, Praveen ^a   Jemec, Domen B ^a   Ding, Feng ^a  

^a CLEMSON UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

LIGANDS;

ACCURATE ESTIMATION; BINDING AFFINITIES; CONFORMATIONAL CHANGE; INTERMOLECULAR ENERGY; INTERMOLECULAR INTERACTION ENERGIES; INTRAMOLECULAR ENERGY; RANKING AND SELECTION; RECEPTOR FLEXIBILITY;

BINDING ENERGY;

LIGAND; PROTEIN; PROTEIN BINDING;

BENCHMARKING; CHEMISTRY; METABOLISM; MOLECULAR DOCKING; PROTEIN CONFORMATION; STRUCTURE ACTIVITY RELATION;

BENCHMARKING; LIGANDS; MOLECULAR DOCKING SIMULATION; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEINS; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 84976420300     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/acs.jcim.5b00303     Document Type: Article

References (44)

1. Bursulaya, B.; Totrov, M.; Abagyan, R.; Brooks, C. Comparative Study of Several Algorithms for Flexible Ligand Docking J. Comput.-Aided Mol. Des. 2003, 17 (11) 755-763 10.1023/B:JCAM.0000017496.76572.6f
2. Totrov, M.; Abagyan, R. Flexible Ligand Docking to Multiple Receptor Conformations: A Practical Alternative Curr. Opin. Struct. Biol. 2008, 18 (2) 178-184 10.1016/j.sbi.2008.01.004
3. Teodoro, M.; Kavraki, L. Conformational Flexibility Models for the Receptor in Structure Based Drug Design Curr. Pharm. Des. 2003, 9, 1635-1648 10.2174/1381612033454595
4. Cozzini, P.; Kellogg, G. E.; Spyrakis, F.; Abraham, D. J.; Costantino, G.; Emerson, A.; Fanelli, F.; Gohlke, H.; Kuhn, L. A.; Morris, G. M.; Orozco, M.; Pertinhez, T. A.; Rizzi, M.; Sotriffer, C. Target Flexibility J. Med. Chem. 2008, 51 (20) 6237-6255 10.1021/jm800562d
5. Jiang, F.; Kim, S. H. Soft Docking": Matching of Molecular Surface Cubes J. Mol. Biol. 1991, 219 (1) 79-102 10.1016/0022-2836(91)90859-5
6. Anderson, A. C.; O'Neil, R. H.; Surti, T. S.; Stroud, R. M. Approaches to Solving the Rigid Receptor Problem by Identifying a Minimal Set of Flexible Residues during Ligand Docking Chem. Biol. 2001, 8 (5) 445-457 10.1016/S1074-5521(01)00023-0
7. Kairys, V.; Gilson, M. K. Enhanced Docking with the Mining Minima Optimizer: Acceleration and Side-Chain Flexibility J. Comput. Chem. 2002, 23 (16) 1656-1670 10.1002/jcc.10168
8. 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
9. Barril, X.; Morley, S. D. Unveiling the Full Potential of Flexible Receptor Docking Using Multiple Crystallographic Structures J. Med. Chem. 2005, 48 (13) 4432-4443 10.1021/jm048972v
10. Sheridan, R. P.; McGaughey, G. B.; Cornell, W. D. Multiple Protein Structures and Multiple Ligands: Effects on the Apparent Goodness of Virtual Screening Results J. Comput.-Aided Mol. Des. 2008, 22 (3-4) 257-265 10.1007/s10822-008-9168-9
11. Knegtel, R. M.; Kuntz, I. D.; Oshiro, C. M. Molecular Docking to Ensembles of Protein Structures J. Mol. Biol. 1997, 266 (2) 424-440 10.1006/jmbi.1996.0776
12. Damm, K. L.; Carlson, H. A. Exploring Experimental Sources of Multiple Protein Conformations in Structure-Based Drug Design J. Am. Chem. Soc. 2007, 129 (26) 8225-8235 10.1021/ja0709728
13. Koska, J.; Spassov, V. Z.; Maynard, A. J.; Yan, L.; Austin, N.; Flook, P. K.; Venkatachalam, C. M. Fully Automated Molecular Mechanics Based Induced Fit Protein-Ligand Docking Method J. Chem. Inf. Model. 2008, 48 (10) 1965-1973 10.1021/ci800081s
14. Cheng, L. S.; Amaro, R. E.; Xu, D.; Li, W. W.; Arzberger, P. W.; McCammon, J. A. Ensemble-Based Virtual Screening Reveals Potential Novel Antiviral Compounds for Avian Influenza Neuraminidase J. Med. Chem. 2008, 51 (13) 3878-3894 10.1021/jm8001197
15. Soliva, R.; Gelpí, J. L.; Almansa, C.; Virgili, M.; Orozco, M. Dissection of the Recognition Properties of p38 MAP Kinase. Determination of the Binding Mode of a New Pyridinyl-Heterocycle Inhibitor Family J. Med. Chem. 2007, 50 (2) 283-293 10.1021/jm061073h
16. Fan, H.; Irwin, J. J.; Webb, B. M.; Klebe, G.; Shoichet, B. K.; Sali, A. Molecular Docking Screens Using Comparative Models of Proteins J. Chem. Inf. Model. 2009, 49 (11) 2512-2527 10.1021/ci9003706
17. Keserû, G. M.; Kolossváry, I. Fully Flexible Low-Mode Docking: Application to Induced Fit in HIV Integrase J. Am. Chem. Soc. 2001, 123 (50) 12708-12709 10.1021/ja0160086
18. Rueda, M.; Bottegoni, G.; Abagyan, R. Consistent Improvement of Cross-Docking Results Using Binding Site Ensembles Generated with Elastic Network Normal Modes J. Chem. Inf. Model. 2009, 49 (3) 716-725 10.1021/ci8003732
19. Novoa, E. M.; Pouplana, L. R. de; Barril, X.; Orozco, M. Ensemble Docking from Homology Models J. Chem. Theory Comput. 2010, 6 (8) 2547-2557 10.1021/ct100246y
20. Chaudhuri, R.; Carrillo, O.; Laughton, C. A.; Orozco, M. Application of Drug-Perturbed Essential Dynamics/Molecular Dynamics (ED/MD) to Virtual Screening and Rational Drug Design J. Chem. Theory Comput. 2012, 8 (7) 2204-2214 10.1021/ct300223c
21. Davis, I. W.; Baker, D. RosettaLigand Docking with Full Ligand and Receptor Flexibility J. Mol. Biol. 2009, 385 (2) 381-392 10.1016/j.jmb.2008.11.010
22. Ding, F.; Yin, S.; Dokholyan, N. V. Rapid Flexible Docking Using a Stochastic Rotamer Library of Ligands J. Chem. Inf. Model. 2010, 50 (9) 1623-1632 10.1021/ci100218t
23. Ding, F.; Dokholyan, N. V. Incorporating Backbone Flexibility in MedusaDock Improves Ligand-Binding Pose Prediction in the CSAR2011 Docking Benchmark J. Chem. Inf. Model. 2013, 53 (8) 1871-1879 10.1021/ci300478y
24. KIM, R.; SKOLNICK, J. Assessment of Programs for Ligand Binding Affinity Prediction J. Comput. Chem. 2008, 29 (8) 1316-1331 10.1002/jcc.20893
25. Damm-Ganamet, K. L.; Smith, R. D.; Dunbar, J. B.; Stuckey, J. A.; Carlson, H. A. CSAR Benchmark Exercise 2011-2012: Evaluation of Results from Docking and Relative Ranking of Blinded Congeneric Series J. Chem. Inf. Model. 2013, 53 (8) 1853-1870 10.1021/ci400025f
26. Armen, R. S.; Chen, J.; Brooks, C. L. An Evaluation of Explicit Receptor Flexibility in Molecular Docking Using Molecular Dynamics and Torsion Angle Molecular Dynamics J. Chem. Theory Comput. 2009, 5 (10) 2909-2923 10.1021/ct900262t
27. Kolb, P.; Huang, D.; Dey, F.; Caflisch, A. Discovery of Kinase Inhibitors by High-Throughput Docking and Scoring Based on a Transferable Linear Interaction Energy Model J. Med. Chem. 2008, 51 (5) 1179-1188 10.1021/jm070654j
28. Yin, S.; Biedermannova, L.; Vondrasek, J.; Dokholyan, N. V. MedusaScore: An Accurate Force Field-Based Scoring Function for Virtual Drug Screening J. Chem. Inf. Model. 2008, 48 (8) 1656-1662 10.1021/ci8001167
29. Ding, F.; Dokholyan, N. V. Emergence of Protein Fold Families through Rational Design PLoS Comput. Biol. 2006, 2 (7) e85 10.1371/journal.pcbi.0020085
30. Huang, N.; Shoichet, B. K.; Irwin, J. J. Benchmarking Sets for Molecular Docking J. Med. Chem. 2006, 49 (23) 6789-6801 10.1021/jm0608356
31. 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
32. Dunbrack, R. L., Jr; Karplus, M. Backbone-Dependent Rotamer Library for Proteins Application to Side-Chain Prediction J. Mol. Biol. 1993, 230 (2) 543-574 10.1006/jmbi.1993.1170
33. Neria, E.; Fischer, S.; Karplus, M. Simulation of Activation Free Energies in Molecular Systems J. Chem. Phys. 1996, 105, 1902 10.1063/1.472061
34. Lazaridis, T. Effective Energy Function for Proteins in Lipid Membranes Proteins: Struct., Funct., Genet. 2003, 52 (2) 176-192 10.1002/prot.10410
35. Lazaridis, T.; Karplus, M. Effective Energy Functions for Protein Structure Prediction Curr. Opin. Struct. Biol. 2000, 10 (2) 139-145 10.1016/S0959-440X(00)00063-4
36. Kortemme, T.; Morozov, A. V.; Baker, D. An Orientation-Dependent Hydrogen Bonding Potential Improves Prediction of Specificity and Structure for Proteins and Protein-Protein Complexes J. Mol. Biol. 2003, 326 (4) 1239-1259 10.1016/S0022-2836(03)00021-4
37. Yin, S.; Ding, F.; Dokholyan, N. V. Eris: An Automated Estimator of Protein Stability Nat. Methods 2007, 4 (6) 466-467 10.1038/nmeth0607-466
38. O'Boyle, N. M.; Banck, M.; James, C. A.; Morley, C.; Vandermeersch, T.; Hutchison, G. R. Open Babel: An Open Chemical Toolbox J. Cheminf. 2011, 3 (1) 33 10.1186/1758-2946-3-33
39. Gilbert, K.; Guha, R. smi23d-3D Coordinate Generation. Http://sourceforge.net/p/cicc-grid/code/HEAD/tree/cicc-grid/smi23d/ (accessed August 1, 2015).
40. Halgren, T. A. MMFF VI. MMFF94s Option for Energy Minimization Studies J. Comput. Chem. 1999, 20 (7) 720-729 10.1002/(SICI)1096-987X(199905)20:7<720::AID-JCC7>3.0.CO;2-X
41. Berman, H. M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T. N.; Weissig, H.; Shindyalov, I. N.; Bourne, P. E. The Protein Data Bank Nucleic Acids Res. 2000, 28 (1) 235-242 10.1093/nar/28.1.235
42. Altschul, S. F.; Madden, T. L.; Schäffer, A. A.; Zhang, J.; Zhang, Z.; Miller, W.; Lipman, D. J. Gapped BLAST and PSI-BLAST: A New Generation of Protein Database Search Programs Nucleic Acids Res. 1997, 25 (17) 3389-3402 10.1093/nar/25.17.3389
43. Tinberg, C. E.; Khare, S. D.; Dou, J.; Doyle, L.; Nelson, J. W.; Schena, A.; Jankowski, W.; Kalodimos, C. G.; Johnsson, K.; Stoddard, B. L.; Baker, D. Computational Design of Ligand-Binding Proteins with High Affinity and Selectivity Nature 2013, 501 (7466) 212-216 10.1038/nature12443
44. Gilli, P.; Ferretti, V.; Gilli, G.; Borea, P. A. Enthalpy-Entropy Compensation in Drug-Receptor Binding J. Phys. Chem. 1994, 98 (5) 1515-1518 10.1021/j100056a024