Collective variable driven molecular dynamics to improve protein-protein docking scoring

Computational Biology and Chemistry

Volumn 49, Issue , 2014, Pages 1-6

  Masone, Diego ^a   Grosdidier, Solène ^b  

^a Facultad de Ciencias Naturales e Instituto M Lillo   (Argentina)

^b UNIVERSITAT POMPEU FABRA   (Spain)

Author keywords

Collective variable; Docking; Molecular dynamics; Protein protein; Scoring

Indexed keywords

COLLECTIVE VARIABLES; MOLECULAR DYNAMICS SIMULATIONS; NEAR-NATIVE CONFORMATIONS; PROTEIN-PROTEIN; PROTEIN-PROTEIN COMPLEXES; PROTEIN-PROTEIN DOCKING; PROTEIN-PROTEIN INTERFACE; SCORING;

CONFORMATIONS; DOCKING; HYDROGEN BONDS; MOLECULAR DYNAMICS;

PROTEINS;

PROTEIN;

CHEMISTRY; HYDROGEN BOND; METABOLISM; MOLECULAR DYNAMICS;

HYDROGEN BONDING; MOLECULAR DYNAMICS SIMULATION; PROTEINS;

EID: 84893587853     PISSN: 14769271     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.compbiolchem.2013.12.003     Document Type: Article

References (47)

1. C.F. Abrams, and E. Vanden-Eijnden Large-scale conformational sampling of proteins using temperature-accelerated molecular dynamics Proceedings of the National Academy of Sciences of the United States of America 107 11 2010 4961 4966
2. H. Alonso, A.A. Bliznyuk, and J.E. Gready Combining docking and molecular dynamic simulations in drug design Medicinal Research Reviews 26 5 2006 531 568 (Pubitemid 44230412)
3. J. Atkins, and W.E. Hart On the intractability of the protein folding with finite alphabet of amino-acids Journal of Computational Biology 5 3 1999 423 466
4. H.J.C. Berendsen, J.P.M. Postma, W.F. van Gunsteren, A. DiNola, and J.R. Haak Molecular dynamics with coupling to an external bath Journal of Chemical Physics 81 1984 3684 3690
5. M. Bonomi, D. Branduardi, G. Bussi, C. Camilloni, D. Provasi, P. Raiteri, D. Donadio, F. Marinelli, F. Pietrucci, R.A. Broglia, and M. Parrinello PLUMED: a portable plugin for free energy calculations with molecular dynamics Computer Physics Communications 180 2009 1961
6. K.W. Borrelli, B. Cossins, and V. Guallar Exploring hierarchical refinement techniques for induced fit docking with protein and ligand flexibility Journal of Computational Chemistry 31 2010 1224 1235
7. K.W. Borrelli, A. Vitalis, R. Alcantara, and V. Guallar Protein energy landscape exploration. A novel Monte Carlo technique, implications on camphor ligand binding Journal of Chemical Theory and Computation 6 2005 1304 1311
8. P.Y. Calland On the structural complexity of a protein Protein Engineering 16 2 2003 76 86
9. C. Camacho, and S. Vajda Protein docking along smooth association pathways Proceedings of the National Academy of Sciences of the United States of America 98 2001 10636 10641 (Pubitemid 32878673)
10. R. Chen, J. Mintseris, J. Janin, and Z. Weng A protein-protein docking benchmark Proteins 52 2003 88 91 (Pubitemid 36648855)
11. P. Crescenzi, D. Goldman, C.H. Papadimitriou, A. Piccolboni, and M. Yannakakis On the complexity of protein folding Journal of Computational Biology 5 3 1998 423 466
12. D.J. Diller, and C.L. Verlinde A critical evaluation of several global optimization algorithms for the purpose of molecular docking Journal of Computational Chemistry 20 1999 1740 1751 (Pubitemid 129652401)
13. T.M. Cheng, T.L. Blundell, and J. Fernandez-Recio pyDock: electrostatics and desolvation for effective scoring of rigid-body protein-protein docking Proteins 68 2007 503 515 (Pubitemid 46981943)
14. P. Cozzini, G.E. Kellogg, F. Spyrakis, D.J. Abraham, G. Costantino, A. Emerson, F. Fanelli, H. Gohlke, L.A. Kuhn, G.M. Morris, M. Orozco, T.A. Pertinhez, M. Rizzi, and C.A. Sotriffer Target flexibility: an emerging consideration in drug discovery and design Journal of Medicinal Chemistry 51 20 2008 6237 6255
15. J.S. Dixon Evaluation of the CASP2 docking section Proteins 29 1 1997 198 204 (Pubitemid 28090499)
16. F. Fabiola, R. Bertram, A. Korostelev, and M.S. Chapman An improved hydrogen bond potential: Impact on medium resolution protein structures Protein Science 11 6 2002 1415 1423 (Pubitemid 34547213)
17. G. Fiorin, M.L. Klein, and J. Hénin Using collective variables to drive molecular dynamics simulations Molecular Physics 2013 1 18
18. H.A. Gabb, R.M. Jackson, and M.J.E. Sternberg Modelling protein docking using shape complementarity, electrostatics and biochemical information Journal of Molecular Biology 272 1997 106 120 (Pubitemid 27395541)
19. A.T. Hagler, E. Huler, and S. Lifson Energy functions for peptides and proteins. i. Derivation of a consistent including the hydrogen bond from amide crystals Journal of the American Chemical Society 96 17 1974 5319 5327
20. A.T. Hagler, and S. Lifson Energy functions for peptides and proteins. ii. The amine hydrogen bond and calculation of amide crystal properties Journal of the American Chemical Society 96 17 1974 5327 5335
21. I. Halperin, B. Ma, H. Wolfson, and R. Nussinov Principles of docking: an overview of search algorithms and a guide to scoring functions Proteins 47 2002 409 443 (Pubitemid 34614722)
22. B. Hess, H. Bekker, H.J.C. Berendsen, and J.G.E.M.J. Fraaije LINCS: a linear constraint solver for molecular simulations Computers and Chemistry 18 12 1997 1463 1472 (Pubitemid 127637344)
23. B. Hess, C. Kutzner, D. van der Spoel, and E. Lindahl GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation Journal of Chemical Theory and Computation 4 2008 435 447
24. H. Hu, M. Elstner, and J. Hermans Comparison of a QM/MM force field and molecular mechanics force fields in simulations of alanine and glycine "dipeptides" (Ace-Ala-Nme and Ace-Gly-Nme) in water in relation to the problem of modeling the unfolded peptide backbone in solution Proteins 50 2003 451 463 (Pubitemid 36158458)
25. W. Humphrey, A. Dalke, and K. Schulten VMD - visual molecular dynamics Journal of Molecular Graphics 14 1 1996 33 38
26. H. Hwang, T. Vreven, B. Pierce, J. Hung, and Z. Weng Performance of ZDOCK and ZRANK in CAPRI round 13-19 Proteins 78 15 2010 3104 3110
27. H. Hwang, T. Vreven, J. Janin, and Z. Weng Protein-protein docking benchmark version 4.0 Proteins 78 15 2010 3111 3114
28. M. Król, R.A. Chaleil, A.L. Tournier, and P.A. Bates Implicit flexibility in protein docking: cross-docking and local refinement Proteins 69 4 2007 750 757 (Pubitemid 350210134)
29. M. Król, A.L. Tournier, and P.A. Bates Flexible relaxation of rigid-body docking solutions Proteins 68 1 2007 159 169 (Pubitemid 46871590)
30. S. Kumar, P.W. Payne, and M. Vasquez Method for free-energy calculations using iterative techniques Journal of Computational Chemistry 17 1996 1269 1275 (Pubitemid 126562032)
31. A. Laio, and F.L. Gervasio Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science Reports on Progress in Physics 71 2008 126601
32. A. Laio, and M. Parrinello Escaping free-energy minima Proceedings of the National Academy of Sciences of the United States of America 99 20 2002 12562 12566
33. J.H. Lii, and N.L. Allinger Directional hydrogen bonding in the MM3 force field. I Journal of Physical Organic Chemistry 7 1994 591 609
34. J.H. Lii, and N.L. Allinger Directional hydrogen bonding in the MM3 force field. II Journal of Computational Chemistry 19 1998 1001 1016 (Pubitemid 128598740)
35. S. Lindert, J. Meiler, and J.A. McCammon Iterative molecular dynamics - Rosetta protein structure refinement protocol to improve model quality Journal of Chemical Theory and Computation 9 8 2013 3843 3847
36. S. Liu, Y. Gao, and I.A. Vakser Dockground protein-protein docking decoy set Bioinformatics 24 22 2008 2634 2635
37. W. Luo, J. Pei, and Y. Zhu A fast protein-ligand docking algorithm based on hydrogen bond matching and surface shape complementarity Journal of Molecular Modeling 16 5 2010 903 913
38. D. Masone, F. Ciocco Aloia, and M.G. Del Pópolo H-bond refinement for electron transfer membrane-bound protein-protein complexes: cytochrome c oxidase and cytochrome c552 Computational Biology and Chemistry 47 2013 31 36
39. D. Masone, I. Cabeza de Vaca, C. Pons, J. Fernández Recio, and V. Guallar H-bond network optimization in protein-protein complexes: are all-atom force field scores enough? Proteins 80 3 2012 818 824
40. A.V. Morozov, T. Kortemme, K. Tsemekhman, and D. Baker Close agreement between the orientation dependence of hydrogen bonds observed in protein structures and quantum mechanical calculations Proceedings of the National Academy of Sciences of the United States of America 101 18 2004 6946 6951 (Pubitemid 38596423)
41. A.T. Phillips, J.B. Rosen, and K.A. Dill Convex global underestimation for molecular structure prediction From Local to Global Optimization: Nonconvex Optimization and Its Applications 53 2001 1 18
42. A. Samiotakis, D. Homouz, and M.S. Cheung Multiscale investigation of chemical interference in proteins Journal of Chemical Physics 132 2010 175101
43. G.R. Smith, and M.J.E. Sternberg Prediction of protein-protein interactions by docking methods Current Opinion in Structural Biology 12 2002 28 35 (Pubitemid 34142717)
44. P. Tiwary, and A. van de Walle Accelerated molecular dynamics through stochastic iterations and collective variable based basin identification Physical Review B 87 2013 094304
45. M. Totrov, and R. Abagyan Flexible protein-ligand docking by global energy optimization in internal coordinates Proteins 1 1997 215 220 (Pubitemid 28090502)
46. A. Tovchigrechko, and I.A. Vakser GRAMM-X public web server for protein-protein docking Nucleic Acids Research 34 2006 310 314
47. G.M. Verkhivker, D. Bouzida, D.K. Gehlhaar, P.A. Rejto, S. Arthurs, A.B. Colson, S.T. Freer, V. Larson, B.A. Luty, T. Marrone, and P.W. Rose Deciphering common failures in molecular docking of ligand-protein complexes Journal of Computer-Aided Materials Design 14 2000 731 751