-
1
-
-
41949111630
-
Recent progress and future directions in protein-protein docking
-
Ritchie DW, (2008) Recent progress and future directions in protein-protein docking. Curr Protein Pept Sc 9: 1-15.
-
(2008)
Curr Protein Pept Sc
, vol.9
, pp. 1-15
-
-
Ritchie, D.W.1
-
2
-
-
0036468385
-
Prediction of protein-protein interactions by docking methods
-
Smith GR, Sternberg MJE, (2002) Prediction of protein-protein interactions by docking methods. Curr Opin Struc Biol 12: 28-35.
-
(2002)
Curr Opin Struc Biol
, vol.12
, pp. 28-35
-
-
Smith, G.R.1
Sternberg, M.J.E.2
-
3
-
-
0035040480
-
Protein docking using continuum electrostatics and geometric fit
-
Mandell JG, Roberts VA, Pique ME, Kotlovyi V, Mitchell JC, et al. (2001) Protein docking using continuum electrostatics and geometric fit. Protein Eng 14: 105-13.
-
(2001)
Protein Eng
, vol.14
, pp. 105-113
-
-
Mandell, J.G.1
Roberts, V.A.2
Pique, M.E.3
Kotlovyi, V.4
Mitchell, J.C.5
-
4
-
-
0026572775
-
Molecular-surface recognition - Determination of geometric fit between protein and their ligands by correlation techniques
-
Katchalskikatzir E, Shariv I, Eisenstein M, Friesem AA, Aflalo C, et al. (1992) Molecular-surface recognition- Determination of geometric fit between protein and their ligands by correlation techniques. Proceedings of the National Academy of Sciences of the United States of America 89: 2195-9.
-
(1992)
Proceedings of the National Academy of Sciences of the United States of America
, vol.89
, pp. 2195-2199
-
-
Katchalskikatzir, E.1
Shariv, I.2
Eisenstein, M.3
Friesem, A.A.4
Aflalo, C.5
-
5
-
-
0031565730
-
Modelling protein docking using shape complementarity, electrostatics and biochemical information
-
Gabb HA, Jackson RM, Sternberg MJE, (1997) Modelling protein docking using shape complementarity, electrostatics and biochemical information. J Mol Biol 272: 106-20.
-
(1997)
J Mol Biol
, vol.272
, pp. 106-120
-
-
Gabb, H.A.1
Jackson, R.M.2
Sternberg, M.J.E.3
-
6
-
-
0033587727
-
A systematic study of low-resolution recognition in protein-protein complexes
-
Vakser IA, Matar OG, Lam CF, (1999) A systematic study of low-resolution recognition in protein-protein complexes. P Natl Acad Sci USA 96: 8477-82.
-
(1999)
P Natl Acad Sci USA
, vol.96
, pp. 8477-8482
-
-
Vakser, I.A.1
Matar, O.G.2
Lam, C.F.3
-
7
-
-
0029089732
-
Molecular-surface complementarity at protein-protein interfaces - the critical role played by surface normals at well placed, sparse, points in docking
-
Norel R, Lin SL, Wolfson HJ, Nussinov R, (1995) Molecular-surface complementarity at protein-protein interfaces- the critical role played by surface normals at well placed, sparse, points in docking. J Mol Biol 252: 263-73.
-
(1995)
J Mol Biol
, vol.252
, pp. 263-273
-
-
Norel, R.1
Lin, S.L.2
Wolfson, H.J.3
Nussinov, R.4
-
8
-
-
84860388898
-
Integrating atom-based and residue-based scoring functions for protein-protein docking
-
Vreven T, Hwang H, Weng Z, (2011) Integrating atom-based and residue-based scoring functions for protein-protein docking. Protein Sci 20: 1576-86.
-
(2011)
Protein Sci
, vol.20
, pp. 1576-1586
-
-
Vreven, T.1
Hwang, H.2
Weng, Z.3
-
9
-
-
34248513078
-
ZRANK: Reranking protein docking predictions with an optimized energy function
-
Pierce B, Weng Z, (2007) ZRANK: Reranking protein docking predictions with an optimized energy function. Proteins 67: 1078-86.
-
(2007)
Proteins
, vol.67
, pp. 1078-1086
-
-
Pierce, B.1
Weng, Z.2
-
11
-
-
77449134208
-
PIE-efficient filters and coarse grained potentials for unbound protein-protein docking
-
Ravikant DVS, Elber R, (2010) PIE-efficient filters and coarse grained potentials for unbound protein-protein docking. Proteins 78: 400-19.
-
(2010)
Proteins
, vol.78
, pp. 400-419
-
-
Ravikant, D.V.S.1
Elber, R.2
-
12
-
-
55449101982
-
Protein Docking by the Underestimation of Free Energy Funnels in the Space of Encounter Complexes
-
Shen Y, Paschalidis IC, Vakili P, Vajda S, (2008) Protein Docking by the Underestimation of Free Energy Funnels in the Space of Encounter Complexes. Plos Comput Biol 4: e1000191.
-
(2008)
Plos Comput Biol
, vol.4
-
-
Shen, Y.1
Paschalidis, I.C.2
Vakili, P.3
Vajda, S.4
-
13
-
-
38949083887
-
Funnel hunting in a rough terrain: Learning and discriminating native energy funnels
-
London N, Schueler-Furman O, (2008) Funnel hunting in a rough terrain: Learning and discriminating native energy funnels. Structure 16: 269-79.
-
(2008)
Structure
, vol.16
, pp. 269-279
-
-
London, N.1
Schueler-Furman, O.2
-
14
-
-
59149107086
-
FunHunt: model selection based on energy landscape characteristics
-
London N, Schueler-Furman O, (2008) FunHunt: model selection based on energy landscape characteristics. Biochem Soc T 36: 1418-21.
-
(2008)
Biochem Soc T
, vol.36
, pp. 1418-1421
-
-
London, N.1
Schueler-Furman, O.2
-
15
-
-
79960075532
-
A machine learning approach for the prediction of protein surface loop flexibility
-
Hwang H, Vreven T, Whitfield TW, Wiehe K, Weng Z, (2011) A machine learning approach for the prediction of protein surface loop flexibility. Proteins 79: 2467-74.
-
(2011)
Proteins
, vol.79
, pp. 2467-2474
-
-
Hwang, H.1
Vreven, T.2
Whitfield, T.W.3
Wiehe, K.4
Weng, Z.5
-
16
-
-
0038161052
-
Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations
-
Gray JJ, Moughon S, Wang C, Schueler-Furman O, Kuhlman B, et al. (2003) Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. J Mol Biol 331: 281-99.
-
(2003)
J Mol Biol
, vol.331
, pp. 281-299
-
-
Gray, J.J.1
Moughon, S.2
Wang, C.3
Schueler-Furman, O.4
Kuhlman, B.5
-
17
-
-
44949117092
-
A combination of rescoring and refinement significantly improves protein docking performance
-
Pierce B, Weng Z, (2008) A combination of rescoring and refinement significantly improves protein docking performance. Proteins 72: 270-9.
-
(2008)
Proteins
, vol.72
, pp. 270-279
-
-
Pierce, B.1
Weng, Z.2
-
18
-
-
52249122794
-
Principles of flexible protein-protein docking
-
Andrusier N, Mashiach E, Nussinov R, Wolfson HJ, (2008) Principles of flexible protein-protein docking. Proteins 73: 271-89.
-
(2008)
Proteins
, vol.73
, pp. 271-289
-
-
Andrusier, N.1
Mashiach, E.2
Nussinov, R.3
Wolfson, H.J.4
-
19
-
-
77951297973
-
Accounting for conformational changes during protein-protein docking
-
Zacharias M, (2010) Accounting for conformational changes during protein-protein docking. Curr Opin Struc Biol 20: 180-6.
-
(2010)
Curr Opin Struc Biol
, vol.20
, pp. 180-186
-
-
Zacharias, M.1
-
20
-
-
0038526303
-
ZDOCK: An initial-stage protein-docking algorithm
-
Chen R, Li L, Weng Z, (2003) ZDOCK: An initial-stage protein-docking algorithm. Proteins 52: 80-7.
-
(2003)
Proteins
, vol.52
, pp. 80-87
-
-
Chen, R.1
Li, L.2
Weng, Z.3
-
21
-
-
0037093643
-
Docking unbound proteins using shape complementarity, desolvation, and electrostatics
-
Chen R, Weng Z, (2002) Docking unbound proteins using shape complementarity, desolvation, and electrostatics. Proteins 47: 281-94.
-
(2002)
Proteins
, vol.47
, pp. 281-294
-
-
Chen, R.1
Weng, Z.2
-
22
-
-
35449008122
-
Integrating statistical pair potentials into protein complex prediction
-
Mintseris J, Pierce B, Wiehe K, Anderson R, Chen R, et al. (2007) Integrating statistical pair potentials into protein complex prediction. Proteins 69: 511-20.
-
(2007)
Proteins
, vol.69
, pp. 511-520
-
-
Mintseris, J.1
Pierce, B.2
Wiehe, K.3
Anderson, R.4
Chen, R.5
-
23
-
-
80052903046
-
Accelerating Protein Docking in ZDOCK Using an Advanced 3D Convolution Library
-
Pierce BG, Hourai Y, Weng Z, (2011) Accelerating Protein Docking in ZDOCK Using an Advanced 3D Convolution Library. Plos One 6: e24657.
-
(2011)
Plos One
, vol.6
-
-
Pierce, B.G.1
Hourai, Y.2
Weng, Z.3
-
24
-
-
80054899738
-
Community-Wide Assessment of Protein-Interface Modeling Suggests Improvements to Design Methodology
-
Fleishman SJ, Whitehead TA, Strauch EM, Corn JE, Qin SB, et al. (2011) Community-Wide Assessment of Protein-Interface Modeling Suggests Improvements to Design Methodology. J Mol Biol 414: 289-302.
-
(2011)
J Mol Biol
, vol.414
, pp. 289-302
-
-
Fleishman, S.J.1
Whitehead, T.A.2
Strauch, E.M.3
Corn, J.E.4
Qin, S.B.5
-
25
-
-
77957951743
-
Performance of ZDOCK and ZRANK in CAPRI Rounds 13-19
-
Hwang H, Vreven T, Pierce BG, Hung J-H, Weng Z, (2010) Performance of ZDOCK and ZRANK in CAPRI Rounds 13-19. Proteins 78: 3104-10.
-
(2010)
Proteins
, vol.78
, pp. 3104-3110
-
-
Hwang, H.1
Vreven, T.2
Pierce, B.G.3
Hung, J.-H.4
Weng, Z.5
-
26
-
-
84857428250
-
Prediction of protein-protein binding free energies
-
Vreven T, Hwang H, Pierce BG, Weng Z, (2012) Prediction of protein-protein binding free energies. Protein Sci 21: 396-404.
-
(2012)
Protein Sci
, vol.21
, pp. 396-404
-
-
Vreven, T.1
Hwang, H.2
Pierce, B.G.3
Weng, Z.4
-
28
-
-
55549101290
-
Sampling Rotation Groups by Successive Orthogonal Images
-
Mitchell JC, (2008) Sampling Rotation Groups by Successive Orthogonal Images. Siam J Sci Comput 30: 525-47.
-
(2008)
Siam J Sci Comput
, vol.30
, pp. 525-547
-
-
Mitchell, J.C.1
-
29
-
-
77957944014
-
Protein-protein docking benchmark version 4.0
-
Hwang H, Vreven T, Janin J, Weng Z, (2010) Protein-protein docking benchmark version 4.0. Proteins 78: 3111-4.
-
(2010)
Proteins
, vol.78
, pp. 3111-3114
-
-
Hwang, H.1
Vreven, T.2
Janin, J.3
Weng, Z.4
-
30
-
-
0028961335
-
Scop - a Structural Classification of Proteins Database for the Investigation of Sequences and Structures
-
Murzin AG, Brenner SE, Hubbard T, Chothia C, (1995) Scop- a Structural Classification of Proteins Database for the Investigation of Sequences and Structures. J Mol Biol 247: 536-40.
-
(1995)
J Mol Biol
, vol.247
, pp. 536-540
-
-
Murzin, A.G.1
Brenner, S.E.2
Hubbard, T.3
Chothia, C.4
-
31
-
-
0345832301
-
ClusPro: an automated docking and discrimination method for the prediction of protein complexes
-
Comeau SR, Gatchell DW, Vajda S, Camacho CJ, (2003) ClusPro: an automated docking and discrimination method for the prediction of protein complexes. Bioinformatics 20: 45-50.
-
(2003)
Bioinformatics
, vol.20
, pp. 45-50
-
-
Comeau, S.R.1
Gatchell, D.W.2
Vajda, S.3
Camacho, C.J.4
|