-
1
-
-
21644469377
-
Assessment of capri predictions in rounds 3-5 shows progress in docking procedures
-
Mendez R, Laplae R, Lensink MF, Wodak SJ. Assessment of capri predictions in rounds 3-5 shows progress in docking procedures. Proteins 2005;60:150-169.
-
(2005)
Proteins
, vol.60
, pp. 150-169
-
-
Mendez, R.1
Laplae, R.2
Lensink, M.F.3
Wodak, S.J.4
-
2
-
-
33646472024
-
High-resolution protein-protein docking
-
Gray JJ. High-resolution protein-protein docking. Curr Opin Struct Biol 2006;16:183-193.
-
(2006)
Curr Opin Struct Biol
, vol.16
, pp. 183-193
-
-
Gray, J.J.1
-
3
-
-
36749006579
-
-
Lensink MF, Mendez R, Wodak SJ. Docking and scoring protein complexes: CAPRI 3rd edition. Proteins 2007;69:704-718.
-
Lensink MF, Mendez R, Wodak SJ. Docking and scoring protein complexes: CAPRI 3rd edition. Proteins 2007;69:704-718.
-
-
-
-
4
-
-
0035838976
-
Automated structure-based prediction of functional sites in proteins: Applications to assessing the validity of inheriting protein function from homology in genome annotation and to protein docking
-
Aloy P, Querol E, Aviles FX, Sternberg MJ. Automated structure-based prediction of functional sites in proteins: applications to assessing the validity of inheriting protein function from homology in genome annotation and to protein docking. J Mol Biol 2001;311: 395-408.
-
(2001)
J Mol Biol
, vol.311
, pp. 395-408
-
-
Aloy, P.1
Querol, E.2
Aviles, F.X.3
Sternberg, M.J.4
-
5
-
-
21644446565
-
Docking prediction using biological information, ZDOCK sampling technique and clusterization guided by the DFIRE statistical energy function
-
Zhang C, Liu S, Zhou Y. Docking prediction using biological information, ZDOCK sampling technique and clusterization guided by the DFIRE statistical energy function. Proteins 2005;60:314-318.
-
(2005)
Proteins
, vol.60
, pp. 314-318
-
-
Zhang, C.1
Liu, S.2
Zhou, Y.3
-
6
-
-
33646044395
-
Whiscy: What information does surface conservation yield? application to data-driven docking
-
deVries SJ, vanDijk AD, Bonvin AM. Whiscy: what information does surface conservation yield? application to data-driven docking. Proteins 2006;63:479-489.
-
(2006)
Proteins
, vol.63
, pp. 479-489
-
-
deVries, S.J.1
vanDijk, A.D.2
Bonvin, A.M.3
-
7
-
-
0031565725
-
Prediction of protein-protein interaction sites using patch analysis
-
Jones S, Thornton JM. Prediction of protein-protein interaction sites using patch analysis. J Mol Biol 1997;272:133-143.
-
(1997)
J Mol Biol
, vol.272
, pp. 133-143
-
-
Jones, S.1
Thornton, J.M.2
-
8
-
-
0035882570
-
Prediction of protein interaction sites from sequence profile and residue neighbor list
-
Zhou H-X, Shan Y. Prediction of protein interaction sites from sequence profile and residue neighbor list. Proteins 2001;44:336-343.
-
(2001)
Proteins
, vol.44
, pp. 336-343
-
-
Zhou, H.-X.1
Shan, Y.2
-
9
-
-
1842526090
-
ProMate: A structure based prediction program to identify the location of protein-protein binding sites
-
Neuvirth H, Raz R, Schreiber G. ProMate: a structure based prediction program to identify the location of protein-protein binding sites. J Mol Biol 2004;338:181-199.
-
(2004)
J Mol Biol
, vol.338
, pp. 181-199
-
-
Neuvirth, H.1
Raz, R.2
Schreiber, G.3
-
10
-
-
33747150197
-
Protein binding site prediction with an empirical scoring function
-
Liang S, Zhang C, Liu S, Zhou Y. Protein binding site prediction with an empirical scoring function. Nucleic Acids Res 2006;34: 3698-3707.
-
(2006)
Nucleic Acids Res
, vol.34
, pp. 3698-3707
-
-
Liang, S.1
Zhang, C.2
Liu, S.3
Zhou, Y.4
-
11
-
-
34548767667
-
Interaction-site prediction for protein complexes: A critical assessment
-
Zhou H-X, Qin S. Interaction-site prediction for protein complexes: a critical assessment. Bioinformatics 2007;23:2203-2209.
-
(2007)
Bioinformatics
, vol.23
, pp. 2203-2209
-
-
Zhou, H.-X.1
Qin, S.2
-
12
-
-
1842595135
-
A novel method for scoring of docked protein complexes using predicted protein-protein binding sites
-
Gottschalk KE, Neuvirth H, Schreiber G. A novel method for scoring of docked protein complexes using predicted protein-protein binding sites. Protein Eng Des Sel 2004;17:183-189.
-
(2004)
Protein Eng Des Sel
, vol.17
, pp. 183-189
-
-
Gottschalk, K.E.1
Neuvirth, H.2
Schreiber, G.3
-
13
-
-
13244277453
-
Physicochemical and residue conservation calculations to improve the ranking of protein-protein docking solutions
-
Duan Y, Reddy BV, Kaznessis YN. Physicochemical and residue conservation calculations to improve the ranking of protein-protein docking solutions. Protein Sci 2005;14:316-328.
-
(2005)
Protein Sci
, vol.14
, pp. 316-328
-
-
Duan, Y.1
Reddy, B.V.2
Kaznessis, Y.N.3
-
14
-
-
28644442113
-
Refinement of unbound protein docking studies using biological knowledge
-
Heusear P, Bau D, Benkert P, Schomburg D. Refinement of unbound protein docking studies using biological knowledge. Proteins 2005;61:1059-1067.
-
(2005)
Proteins
, vol.61
, pp. 1059-1067
-
-
Heusear, P.1
Bau, D.2
Benkert, P.3
Schomburg, D.4
-
15
-
-
21644454183
-
Scoring docking models with evolutionary information
-
Tress M, deJuan D, Grana O, Gomez MJ, Gomez-Puertas P, Gonzalez JM, Lopez G, Valencia A. Scoring docking models with evolutionary information. Proteins 2005;60:275-280.
-
(2005)
Proteins
, vol.60
, pp. 275-280
-
-
Tress, M.1
deJuan, D.2
Grana, O.3
Gomez, M.J.4
Gomez-Puertas, P.5
Gonzalez, J.M.6
Lopez, G.7
Valencia, A.8
-
16
-
-
33645095436
-
Efficient restraints for protein-protein docking by comparison of observed amino acid substitution patterns with those predicted from local environment
-
Chelliah V, Blundell TL, Fernandez-Recio J. Efficient restraints for protein-protein docking by comparison of observed amino acid substitution patterns with those predicted from local environment. J Mol Biol 2006;357:1669-1682.
-
(2006)
J Mol Biol
, vol.357
, pp. 1669-1682
-
-
Chelliah, V.1
Blundell, T.L.2
Fernandez-Recio, J.3
-
17
-
-
0345832301
-
ClusPro: An automated docking and discrimination method for the prediction of protein complexes
-
Comeau SR, Gatchell DW, Vajda S, Camacho CJ. ClusPro: an automated docking and discrimination method for the prediction of protein complexes. Bioinformatics 2004;20:45-50.
-
(2004)
Bioinformatics
, vol.20
, pp. 45-50
-
-
Comeau, S.R.1
Gatchell, D.W.2
Vajda, S.3
Camacho, C.J.4
-
18
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acid Res 1997;25:3389-3402.
-
(1997)
Nucleic Acid Res
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schäffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
19
-
-
0026458378
-
Amino acid substitution matrices from protein blocks
-
Henikoff S, Henikoff J. Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci USA 1992;89:10915-10919.
-
(1992)
Proc Natl Acad Sci USA
, vol.89
, pp. 10915-10919
-
-
Henikoff, S.1
Henikoff, J.2
-
20
-
-
6344291590
-
Prediction of the interaction site on the surface of an isolated protein structure by analysis of side chain energy scores
-
Liang S, Zhang J, Zhang S, Guo H. Prediction of the interaction site on the surface of an isolated protein structure by analysis of side chain energy scores. Proteins 2004;57:548-557.
-
(2004)
Proteins
, vol.57
, pp. 548-557
-
-
Liang, S.1
Zhang, J.2
Zhang, S.3
Guo, H.4
-
21
-
-
0003187567
-
The atomic structure of protein-protein recognition sites
-
Lo Conte L, Chothia C, Janin J. The atomic structure of protein-protein recognition sites. J Mol Biol 1999;285:2177-2198.
-
(1999)
J Mol Biol
, vol.285
, pp. 2177-2198
-
-
Lo Conte, L.1
Chothia, C.2
Janin, J.3
-
22
-
-
21644480883
-
Protein-protein docking benchmark 2.0: An update
-
Mintseris J, Wiehe K, Pierce B, Anderson R, Chen R, Janin J, Weng Z. Protein-protein docking benchmark 2.0: an update. Proteins 2005;60:214-216.
-
(2005)
Proteins
, vol.60
, pp. 214-216
-
-
Mintseris, J.1
Wiehe, K.2
Pierce, B.3
Anderson, R.4
Chen, R.5
Janin, J.6
Weng, Z.7
-
23
-
-
0038526303
-
ZDOCK: An initial-stage protein-docking algorithm
-
Chen R, Li L, Weng Z. ZDOCK: an initial-stage protein-docking algorithm. Proteins 2003;52:80-87.
-
(2003)
Proteins
, vol.52
, pp. 80-87
-
-
Chen, R.1
Li, L.2
Weng, Z.3
-
24
-
-
0038161052
-
Protein-protein docking with simultaneous optimization of rigid body displacement and side chain conformations
-
Gray J, Moughan S, Wang C, Schueler-Furman O, Kuhlman B, Rohl C, Baker D. Protein-protein docking with simultaneous optimization of rigid body displacement and side chain conformations. J Mol Biol 2003;331:281-299.
-
(2003)
J Mol Biol
, vol.331
, pp. 281-299
-
-
Gray, J.1
Moughan, S.2
Wang, C.3
Schueler-Furman, O.4
Kuhlman, B.5
Rohl, C.6
Baker, D.7
-
25
-
-
35449008122
-
Integrating statistical pair potentials into protein complex prediction
-
Mintseris J, Pierce B, Wiehe K, Anderson R, Chen R, Weng Z. Integrating statistical pair potentials into protein complex prediction. Proteins 2007;69:511-520.
-
(2007)
Proteins
, vol.69
, pp. 511-520
-
-
Mintseris, J.1
Pierce, B.2
Wiehe, K.3
Anderson, R.4
Chen, R.5
Weng, Z.6
-
26
-
-
34548811419
-
A simple reference state makes a significant improvement in near-native selections from structurally refined docking decoys
-
Liang S, Liu S, Zhang C, Zhou Y. A simple reference state makes a significant improvement in near-native selections from structurally refined docking decoys. Proteins 2007;69:244-253.
-
(2007)
Proteins
, vol.69
, pp. 244-253
-
-
Liang, S.1
Liu, S.2
Zhang, C.3
Zhou, Y.4
-
27
-
-
34248513078
-
ZRANK:reranking protein docking predictions with an optimized energy function
-
Pierce B, Weng Z. ZRANK:reranking protein docking predictions with an optimized energy function. Proteins 2007;67:1078-1086.
-
(2007)
Proteins
, vol.67
, pp. 1078-1086
-
-
Pierce, B.1
Weng, Z.2
|