Exploring the potential of global protein-protein docking: an overview and critical assessment of current programs for automatic ab initio docking

Drug Discovery Today

Volumn 20, Issue 8, 2015, Pages 969-977

  Huang, Sheng You ^a,b  

^a UNIVERSITY OF MISSOURI   (United States)

^b University of Missouri   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIBODY; ANTIGEN; PROTEIN; PROTEIN BINDING;

AB INITIO CALCULATION; ALGORITHM; ARTICLE; CONFORMATIONAL TRANSITION; MOLECULAR DOCKING; PROTEIN PROTEIN INTERACTION; STATIC ELECTRICITY; ANIMAL; AUTOMATION; CHEMISTRY; COMPUTER AIDED DESIGN; DRUG DESIGN; DRUG DEVELOPMENT; HUMAN; METABOLISM; PROCEDURES; PROTEIN ANALYSIS; PROTEIN CONFORMATION; PROTEIN DOMAIN;

ALGORITHMS; ANIMALS; AUTOMATION; COMPUTER-AIDED DESIGN; DRUG DESIGN; DRUG DISCOVERY; HUMANS; MOLECULAR DOCKING SIMULATION; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN INTERACTION DOMAINS AND MOTIFS; PROTEIN INTERACTION MAPPING; PROTEINS;

EID: 84940614286     PISSN: 13596446     EISSN: 18785832     Source Type: Journal    
DOI: 10.1016/j.drudis.2015.03.007     Document Type: Review

References (88)

1. M.R. Arkin, and J.A. Wells Small-molecule inhibitors of protein-protein interactions: progressing towards the dream Nat. Rev. Drug Discov. 3 2004 301 317
2. M.G. Kann Protein interactions and disease: computational approaches to uncover the etiology of diseases Brief. Bioinform. 8 2007 333 346
3. G. Schreiber, and S.J. Fleishman Computational design of protein-protein interactions Curr. Opin. Struct. Biol. 23 2013 903 910
4. H. Naveed, and J. Liang Weakly stable regions and protein-protein interactions in beta-barrel membrane proteins Curr. Pharm. Des. 20 2014 1268 1273
5. H. Li, and et al. Drug design targeting protein-protein interactions (PPIs) using multiple ligand simultaneous docking (MLSD) and drug repositioning: discovery of raloxifene and bazedoxifene as novel inhibitors of IL-6/GP130 interface J. Med. Chem. 57 2014 632 641
6. H.X. Zhou Theoretical frameworks for multiscale modeling and simulation Curr. Opin. Struct. Biol. 25 2014 67 76
7. J.C. Fuller, and et al. Predicting druggable binding sites at the protein-protein interface Drug Discov. Today 14 2009 155 161
8. S.Y. Huang, and et al. Molecular modeling of the heterodimer of human CFTR's nucleotide-binding domains using a protein-protein docking approach J. Mol. Graph. Model. 27 2009 822 828
9. G. Zhang, and et al. Ion sensing in the RCK1 domain of BK channels Proc. Natl. Acad. Sci. U. S. A. 107 2010 18700 18705
10. L.Q. Zhang, and et al. Interactions between PBEF and oxidative stress proteins - a potential new mechanism underlying PBEF in the pathogenesis of acute lung injury FEBS Lett. 582 2008 1802 1808
11. S. Grosdidier, and J. Fernandez-Recio Protein-protein docking and hot-spot prediction for drug discovery Curr. Pharm. Des. 18 2012 4607 4618
12. S.Y. Huang Search strategies and evaluation in protein-protein docking: principles, advances and challenges Drug Discov. Today 19 2014 1081 1096
13. S.J. Wodak, and J. Janin Computer analysis of protein-protein interaction J. Mol. Biol. 124 1978 323 342
14. G.R. Smith, and M.J. Sternberg Prediction of protein-protein interactions by docking methods Curr. Opin. Struct. Biol. 12 2002 28 35
15. I. Halperin, and et al. Principles of docking: an overview of search algorithms and a guide to scoring functions Proteins 47 2002 409 443
16. D.W. Ritchie Recent progress and future directions in protein-protein docking Curr. Protein Pept. Sci. 9 2008 1 15
17. I.S. Moreira, and et al. Protein-protein docking dealing with the unknown J. Comput. Chem. 31 2010 317 342
18. J. Janin Protein-protein docking tested in blind predictions: the CAPRI experiment Mol. Biosyst. 6 2010 2351 2362
19. S. Vajda, and et al. Sampling and scoring: a marriage made in heaven Proteins 81 2013 1874 1884
20. M. Zacharias Protein-protein docking with a reduced protein model accounting for side-chain flexibility Protein Sci. 12 2003 1271 1282
21. M. Zacharias ATTRACT: protein-protein docking in CAPRI using a reduced protein model Proteins 60 2005 252 256
22. D. Duhovny, and et al. Efficient unbound docking of rigid molecules R. Guido, D. Gusfield, Proceedings of the 2nd Workshop on Algorithms in Bioinformatics (WABI) Rome, Italy Lect. Notes Comput. Sci. 2452 2002 185 200
23. H.A. Gabb, and et al. Modelling protein docking using shape complementarity, electrostatics and biochemical information J. Mol. Biol. 272 1997 106 120
24. I.A. Vakser Evaluation of GRAMM low-resolution docking methodology on the hemagglutinin-antibody complex Proteins Suppl. 1 1997 226 230
25. E. Katchalski-Katzir, and et al. Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques Proc. Natl. Acad. Sci. U. S. A. 89 1992 2195 2199
26. A. Heifetz, and et al. Electrostatics in protein-protein docking Protein Sci. 11 2002 571 587
27. A. Berchanski, and et al. Hydrophobic complementarity in protein-protein docking Proteins 56 2004 130 142
28. J.G. Mandell, and et al. Protein docking using continuum electrostatics and geometric fit Protein Eng. 14 2001 105 113
29. V.A. Roberts, and et al. DOT2: macromolecular docking with improved biophysical models J. Comput. Chem. 34 2013 1743 1758
30. R. Chen, and Z.P. Weng Docking unbound proteins using shape complementarity, desolvation, and electrostatics Proteins 47 2002 281 294
31. R. Chen, and Z. Weng A novel shape complementarity scoring function for protein-protein docking Proteins 51 2003 397 408
32. R. Chen, and et al. ZDOCK: an initial-stage protein docking algorithm Proteins 52 2003 80 87
33. B.G. Pierce, and et al. Accelerating protein docking in ZDOCK using an advanced 3D convolution library PLoS ONE 6 2011 e24657
34. J. Mintseris, and et al. Integrating statistical pair potentials into protein complex prediction Proteins 69 2007 511 520
35. B.G. Pierce, and et al. ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers Bioinformatics 30 2014 1771 1773
36. D. Kozakov, and et al. PIPER: an FFT-based protein docking program with pairwise potentials Proteins 65 2006 392 406
37. C. Zhang, and L. Lai SDOCK: a global protein-protein docking program using stepwise force-field potentials J. Comput. Chem. 32 2011 2598 2612
38. D.W. Ritchie, and G.J. Kemp Protein docking using spherical polar Fourier correlations Proteins 39 2000 178 194
39. D.W. Ritchie, and et al. Accelerating and focusing protein-protein docking correlations using multi-dimensional rotational FFT generating functions Bioinformatics 24 2008 1865 1873
40. J.I. Garzon, and et al. FRODOCK: a new approach for fast rotational protein-protein docking Bioinformatics 25 2009 2544 2551
41. V. Venkatraman, and et al. Protein-protein docking using region-based 3D Zernike descriptors BMC Bioinform. 10 2009 407
42. L. Li, and et al. ASPDock: protein-protein docking algorithm using atomic solvation parameters model BMC Bioinform. 12 2011 36
43. I.H. Moal, and P.A. Bates SwarmDock and the use of normal modes in protein-protein docking Int. J. Mol. Sci. 11 2010 3623 3648
44. C. Bajaj, and et al. F2Dock: fast Fourier protein-protein docking IEEE/ACM Trans. Comput. Biol. Bioinform. 8 2011 45 58
45. J. Janin, and et al. CAPRI: a critical assessment of predicted interactions Proteins 52 2003 2 9
46. R. Mendez, and et al. Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures Proteins 60 2005 150 169
47. M.F. Lensink, and et al. Docking and scoring protein complexes: CAPRI 3rd edition Proteins 69 2007 704 718
48. M.F. Lensink, and S.J. Wodak Blind predictions of protein interfaces by docking calculations in CAPRI Proteins 78 2010 3085 3095
49. M.F. Lensink, and S.J. Wodak Docking, scoring and affinity prediction in CAPRI Proteins 81 2013 2082 2095
50. R. Chen, and et al. A protein-protein docking benchmark Proteins 52 2003 88 91
51. J. Mintseris, and et al. Protein-protein docking benchmark 2.0: an update Proteins 60 2005 214 216
52. H. Hwang, and et al. Protein-protein docking benchmark version 3.0 Proteins 73 2008 705 709
53. H. Hwang, and et al. Protein-protein docking benchmark version 4.0 Proteins 78 2010 3111 3114
54. D. Douguet, and et al. DOCKGROUND resource for studying protein-protein interfaces Bioinformatics 22 2006 2612 2618
55. Y. Gao, and et al. DOCKGROUND system of databases for protein recognition studies: unbound structures for docking Proteins 69 2007 845 851
56. S-Y. Huang, and X. Zou MDockPP: a hierarchical approach for protein-protein docking and its application to CAPRI rounds 15-19 Proteins 78 2010 3096 3103
57. S-.Y. Huang, and et al. Inclusion of the orientational entropic effect and low-resolution experimental information for protein-protein docking in CAPRI Proteins 81 2013 2183 2191
58. T. Vreven, and et al. Integrating atom-based and residue-based scoring functions for protein-protein docking Protein Sci. 20 2011 1576 1586
59. B. Pierce, and Z. Weng ZRANK: reranking protein docking predictions with an optimized energy function Proteins 67 2007 1078 1086
60. B. Pierce, and Z. Weng A combination of rescoring and refinement significantly improves protein docking performance Proteins 72 2008 270 279
61. T.M. Cheng, and et al. pyDock: electrostatics and desolvation for effective scoring of rigid-body protein-protein docking Proteins 68 2007 503 515
62. S. Liang, and et al. A simple reference state makes a significant improvement in near-native selections from structurally refined docking decoys Proteins 69 2007 244 253
63. S-.Y. Huang, and X. Zou An iterative knowledge-based scoring function for protein-protein recognition Proteins 72 2008 557 579
64. S.Y. Huang, and G.K. Springer How the folding funnel depends on size and structure of proteins? A view from the scoring function perspective Tsinghua Sci. Technol. 18 2013 462 468
65. L. Li, and et al. RDOCK: refinement of rigid-body protein docking predictions Proteins 53 2003 693 707
66. N. Andrusier, and et al. FireDock: fast interaction refinement in molecular docking Proteins 69 2007 139 159
67. E. Mashiach, and et al. FiberDock: flexible induced-fit backbone refinement in molecular docking Proteins 78 2010 1503 1519
68. V. Venkatraman, and D.W. Ritchie Flexible protein docking refinement using pose-dependent normal mode analysis Proteins 80 2012 2262 2274
69. M. Krol, and et al. Implicit flexibility in protein docking: cross-docking and local refinement Proteins 69 2007 750 757
70. S. Liang, and et al. Refining near-native protein-protein docking decoys by local re-sampling and energy minimization Proteins 76 2009 309 316
71. S. Viswanath, and et al. Improving ranking of models for protein complexes with side chain modeling and atomic potentials Proteins 81 2013 592 606
72. Y. Shen, and et al. Protein docking by the underestimation of free energy funnels in the space of encounter complexes PLoS Comput. Biol. 4 2008 e1000191
73. Y. Shen Improved flexible refinement of protein docking in CAPRI rounds 22-27 Proteins 81 2013 2129 2136
74. S. Omori, and A. Kitao CyClus: a fast, comprehensive cylindrical interface approximation clustering/reranking method for rigid-body protein-protein docking decoys Proteins 81 2013 1005 1016
75. R. Oliva, and et al. Ranking multiple docking solutions based on the conservation of inter-residue contacts Proteins 81 2013 1571 1584
76. S. Qin, and H.X. Zhou Selection of near-native poses in CAPRI rounds 13-19 Proteins 78 2010 3166 3173
77. S. Qin, and H.X. Zhou Using the concept of transient complex for affinity predictions in CAPRI rounds 20-27 and beyond Proteins 81 2013 2229 2236
78. S. Lorenzen, and Y. Zhang Monte Carlo refinement of rigid-body protein docking structures with backbone displacement and side-chain optimization Protein Sci. 16 2007 2716 2725
79. D. Kozakov, and et al. Discrimination of near-native structures in protein-protein docking by testing the stability of local minima Proteins 72 2008 993 1004
80. N. Kowalsman, and M. Eisenstein Combining interface core and whole interface descriptors in postscan processing of protein-protein docking models Proteins 77 2009 297 318
81. L.C. Xue, and et al. DockRank: ranking docked conformations using partner-specific sequence homology-based protein interface prediction Proteins 82 2014 250 267
82. C. Dominguez, and et al. HADDOCK: a protein-protein docking approach based on biochemical or biophysical information J. Am. Chem. Soc. 125 2003 1731 1737
83. J.J. Gray, and et al. Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations J. Mol. Biol. 331 2003 281 299
84. D.W. Ritchie, and V. Venkatraman Ultra-fast FFT protein docking on graphics processors Bioinformatics 26 2010 2398 2405
85. A. Tovchigrechko, and I.A. Vakser GRAMM-X public web server for protein-protein docking Nucleic Acids Res. 34 2006 W310 W314
86. G. Macindoe, and et al. HexServer: an FFT-based protein docking server powered by graphics processors Nucleic Acids Res. 38 2010 W445 W449
87. D. Schneidman-Duhovny, and et al. PatchDock and SymmDock: servers for rigid and symmetric docking Nucleic Acids Res. 33 2005 W363 W367
88. S.R. Comeau, and et al. ClusPro: a fully automated algorithm for protein-protein docking Nucleic Acids Res. 32 2004 W96 W99