-
1
-
-
0026572775
-
Molecular surface recognition: Determination of geometric fit between proteins and their ligands by correlation techniques
-
Katchalski-Katzir E, Shariv I, Eisenstein M, Friesem AA, Aflalo C, Vakser IA. Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques. Proc Natl Acad Sci USA 1992;89:2195-2199.
-
(1992)
Proc Natl Acad Sci USA
, vol.89
, pp. 2195-2199
-
-
Katchalski-Katzir, E.1
Shariv, I.2
Eisenstein, M.3
Friesem, A.A.4
Aflalo, C.5
Vakser, I.A.6
-
2
-
-
0038185277
-
A novel shape complementarity scoring function for protein-protein docking
-
Chen R, Weng Z. A novel shape complementarity scoring function for protein-protein docking. Proteins 2003;51:397-408.
-
(2003)
Proteins
, vol.51
, pp. 397-408
-
-
Chen, R.1
Weng, Z.2
-
3
-
-
0037093643
-
Docking unbound proteins using shape complementarity, desolvation, and electrostatics
-
Chen R, Weng Z. Docking unbound proteins using shape complementarity, desolvation, and electrostatics. Proteins 2002;47:281-294.
-
(2002)
Proteins
, vol.47
, pp. 281-294
-
-
Chen, R.1
Weng, Z.2
-
4
-
-
0031565730
-
Modelling protein docking using shape complementarity, electrostatics and biochemical information
-
Gabb HA, Jackson RM, Sternberg MJ. Modelling protein docking using shape complementarity, electrostatics and biochemical information. J Mol Biol 1997;272:106-120.
-
(1997)
J Mol Biol
, vol.272
, pp. 106-120
-
-
Gabb, H.A.1
Jackson, R.M.2
Sternberg, M.J.3
-
5
-
-
21644458085
-
Development and testing of an automated approach to protein docking
-
Tovchigrechko A, Vakser IA. Development and testing of an automated approach to protein docking. Proteins 2005;60:296-301.
-
(2005)
Proteins
, vol.60
, pp. 296-301
-
-
Tovchigrechko, A.1
Vakser, I.A.2
-
6
-
-
0242299200
-
RDOCK: Refinement of rigid-body protein docking predictions
-
Li L, Chen R, Weng Z. RDOCK: refinement of rigid-body protein docking predictions. Proteins 2003;53:693-707.
-
(2003)
Proteins
, vol.53
, pp. 693-707
-
-
Li, L.1
Chen, R.2
Weng, Z.3
-
7
-
-
0032512619
-
Rapid refinement of protein interfaces incorporating solvation: Application to the docking problem
-
Jackson RM, Gabb HA, Sternberg MJ. Rapid refinement of protein interfaces incorporating solvation: application to the docking problem. J Mol Biol 1998;276:265-285.
-
(1998)
J Mol Biol
, vol.276
, pp. 265-285
-
-
Jackson, R.M.1
Gabb, H.A.2
Sternberg, M.J.3
-
8
-
-
0033562633
-
Use of pair potentials across protein interfaces in screening predicted docked complexes
-
Mount G, Gabb HA, Sternberg MJ. Use of pair potentials across protein interfaces in screening predicted docked complexes. Proteins 1999;35:364-373.
-
(1999)
Proteins
, vol.35
, pp. 364-373
-
-
Mount, G.1
Gabb, H.A.2
Sternberg, M.J.3
-
9
-
-
0032981961
-
Free energy landscapes of encounter complexes in protein-protein association
-
Camacho CJ, Weng Z, Vajda S, DeLisi C. Free energy landscapes of encounter complexes in protein-protein association. Biophys J 1999;76:1166-1178.
-
(1999)
Biophys J
, vol.76
, pp. 1166-1178
-
-
Camacho, C.J.1
Weng, Z.2
Vajda, S.3
DeLisi, C.4
-
10
-
-
0032530578
-
Clustering of low-energy conformations near the native structures of small proteins
-
Shortle D, Simons KT, Baker D. Clustering of low-energy conformations near the native structures of small proteins. Proc Natl Acad Sci USA 1998;95:11158-11162.
-
(1998)
Proc Natl Acad Sci USA
, vol.95
, pp. 11158-11162
-
-
Shortle, D.1
Simons, K.T.2
Baker, D.3
-
11
-
-
1942519275
-
SPICKER: A clustering approach to identify near-native protein folds
-
Zhang Y, Skolnick J. SPICKER: a clustering approach to identify near-native protein folds. J Comput Chem 2004;25:865-871.
-
(2004)
J Comput Chem
, vol.25
, pp. 865-871
-
-
Zhang, Y.1
Skolnick, J.2
-
12
-
-
0030248996
-
Low-resolution docking: Prediction of complexes for underdetermined structures
-
Vakser IA. Low-resolution docking: prediction of complexes for underdetermined structures. Biopolymers 1996;39:455-464.
-
(1996)
Biopolymers
, vol.39
, pp. 455-464
-
-
Vakser, I.A.1
-
13
-
-
0033587727
-
A systematic study of low-resolution recognition in protein-protein complexes
-
Vakser IA, Matar OG, Lam CF. A systematic study of low-resolution recognition in protein-protein complexes. Proc Natl Acad Sci USA 1999;96:8477-8482.
-
(1999)
Proc Natl Acad Sci USA
, vol.96
, pp. 8477-8482
-
-
Vakser, I.A.1
Matar, O.G.2
Lam, C.F.3
-
14
-
-
0038359612
-
Finding needles in haystacks: Reranking DOT results by using shape complementarity, cluster analysis, and biological information
-
Law DS, Ten Eyck LF, Katzenelson O, Tsigelny I, Roberts VA, Pique ME, Mitchell JC. Finding needles in haystacks: Reranking DOT results by using shape complementarity, cluster analysis, and biological information. Proteins 2003;52:33-40.
-
(2003)
Proteins
, vol.52
, pp. 33-40
-
-
Law, D.S.1
Ten Eyck, L.F.2
Katzenelson, O.3
Tsigelny, I.4
Roberts, V.A.5
Pique, M.E.6
Mitchell, J.C.7
-
15
-
-
0035040480
-
Protein docking using continuum electrostatics and geometric fit
-
Mandell JG, Roberts VA, Pique ME, Kotlovyi V, Mitchell JC, Nelson E, Tsigelny I, Ten Eyck LF. Protein docking using continuum electrostatics and geometric fit. Protein Eng 2001;14:105-113.
-
(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
Nelson, E.6
Tsigelny, I.7
Ten Eyck, L.F.8
-
16
-
-
0038359596
-
Successful discrimination of protein interactions
-
Camacho CJ, Gatchell DW. Successful discrimination of protein interactions. Proteins 2003;52:92-97.
-
(2003)
Proteins
, vol.52
, pp. 92-97
-
-
Camacho, C.J.1
Gatchell, D.W.2
-
17
-
-
3242877815
-
-
Comeau SR, Gatchell DW, Vajda S, Camacho CJ. ClusPro: a fully automated algorithm for protein-protein docking. Nucleic Acids Res 2004;32(Web Server issue):W96-W99.
-
Comeau SR, Gatchell DW, Vajda S, Camacho CJ. ClusPro: a fully automated algorithm for protein-protein docking. Nucleic Acids Res 2004;32(Web Server issue):W96-W99.
-
-
-
-
18
-
-
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
-
19
-
-
21644469377
-
Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures
-
Mendez R, Leplae 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
Leplae, R.2
Lensink, M.F.3
Wodak, S.J.4
-
20
-
-
23244436580
-
Optimal clustering for detecting near-native conformations in protein docking
-
Kozakov D, Clodfelter KH, Vajda S, Camacho CJ. Optimal clustering for detecting near-native conformations in protein docking. Biophys J 2005;89:867-875.
-
(2005)
Biophys J
, vol.89
, pp. 867-875
-
-
Kozakov, D.1
Clodfelter, K.H.2
Vajda, S.3
Camacho, C.J.4
-
21
-
-
0037624841
-
3D-SHOTGUN: A novel, cooperative, fold-recognition meta-predictor
-
Fischer D. 3D-SHOTGUN: a novel, cooperative, fold-recognition meta-predictor. Proteins 2003;51:434-441.
-
(2003)
Proteins
, vol.51
, pp. 434-441
-
-
Fischer, D.1
-
23
-
-
0034780030
-
Peons: A neural-network-based consensus predictor that improves fold recognition
-
Lundstrom J, Rychlewski L, Bujnicki J, Elofsson A. Peons: a neural-network-based consensus predictor that improves fold recognition. Protein Sci 2001;10:2354-2362.
-
(2001)
Protein Sci
, vol.10
, pp. 2354-2362
-
-
Lundstrom, J.1
Rychlewski, L.2
Bujnicki, J.3
Elofsson, A.4
-
24
-
-
33646817694
-
Scoring a diverse set of high-quality docked conformations: A metascore based on electrostatic and desolvation interactions
-
Camacho CJ, Ma H, Champ PC. Scoring a diverse set of high-quality docked conformations: a metascore based on electrostatic and desolvation interactions. Proteins 2006;63:868-877.
-
(2006)
Proteins
, vol.63
, pp. 868-877
-
-
Camacho, C.J.1
Ma, H.2
Champ, P.C.3
-
26
-
-
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
-
27
-
-
33747840389
-
-
Tovchigrechko A, Vakser IA. GRAMM-X public web server for protein-protein docking. Nucleic Acids Res 2006;34(Web Server issue):W310-W314.
-
Tovchigrechko A, Vakser IA. GRAMM-X public web server for protein-protein docking. Nucleic Acids Res 2006;34(Web Server issue):W310-W314.
-
-
-
-
29
-
-
0038359614
-
CAPRI: A critical assessment of predicted interactions
-
Janin J, Henrick K, Moult J, Eyck LT, Sternberg MJ, Vajda S, Vakser I, Wodak SJ. CAPRI: a critical assessment of predicted interactions. Proteins 2003;52:2-9.
-
(2003)
Proteins
, vol.52
, pp. 2-9
-
-
Janin, J.1
Henrick, K.2
Moult, J.3
Eyck, L.T.4
Sternberg, M.J.5
Vajda, S.6
Vakser, I.7
Wodak, S.J.8
-
30
-
-
12944249776
-
A discussion of the solution for the best rotation to relate two sets of vectors
-
Kabsch W. A discussion of the solution for the best rotation to relate two sets of vectors. Acta Crystallogr A 1978;34:827-828.
-
(1978)
Acta Crystallogr A
, vol.34
, pp. 827-828
-
-
Kabsch, W.1
-
31
-
-
10344232638
-
Scoring function for automated assessment of protein structure template quality
-
Zhang Y, Skolnick J. Scoring function for automated assessment of protein structure template quality. Proteins 2004;57:702-710.
-
(2004)
Proteins
, vol.57
, pp. 702-710
-
-
Zhang, Y.1
Skolnick, J.2
|