-
1
-
-
0037442962
-
HADDOCK: a protein-protein docking approach based on biochemical and/or biophysical information
-
Dominguez C, Boelens R, Bonvin AMJJ. HADDOCK: a protein-protein docking approach based on biochemical and/or biophysical information. J Am Chem Soc 2003; 125: 1731-1737.
-
(2003)
J Am Chem Soc
, vol.125
, pp. 1731-1737
-
-
Dominguez, C.1
Boelens, R.2
Bonvin, A.M.J.J.3
-
2
-
-
0038583687
-
Protein-protein docking with a reduced protein model accounting for side-chain flexibility
-
Zacharias M. Protein-protein docking with a reduced protein model accounting for side-chain flexibility. Protein Sci 2003; 12: 1271-1282.
-
(2003)
Protein Sci
, vol.12
, pp. 1271-1282
-
-
Zacharias, M.1
-
3
-
-
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
-
4
-
-
0038021436
-
Assessment of blind predictions of protein-protein interactions: current status of docking methods
-
Mendez R, Leplae R, De Maria L, Wodak SJ. Assessment of blind predictions of protein-protein interactions: current status of docking methods. Proteins 2003; 52: 51-67.
-
(2003)
Proteins
, vol.52
, pp. 51-67
-
-
Mendez, R.1
Leplae, R.2
De Maria, L.3
Wodak, S.J.4
-
5
-
-
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
-
6
-
-
36749006579
-
Docking and scoring protein complexes: CAPRI 3rd Edition
-
Lensink MF, Méndez R, Wodak SJ. Docking and scoring protein complexes: CAPRI 3rd Edition. Proteins 2007; 69: 704-18.
-
(2007)
Proteins
, vol.69
, pp. 704-718
-
-
Lensink, M.F.1
Méndez, R.2
Wodak, S.J.3
-
7
-
-
77950591112
-
Exploring hierarchical refinement techniques for induced fit docking with protein and ligand flexibility
-
Borrelli KW, Cossins B, Guallar V. Exploring hierarchical refinement techniques for induced fit docking with protein and ligand flexibility. J Comp Chem 2010; 31: 1224-1235.
-
(2010)
J Comp Chem
, vol.31
, pp. 1224-1235
-
-
Borrelli, K.W.1
Cossins, B.2
Guallar, V.3
-
8
-
-
34147107263
-
Protein energy landscape exploration. A novel Monte Carlo technique. Implications on camphor ligand binding
-
Borrelli KW, Vitalis A, Alcantara R, Guallar V. Protein energy landscape exploration. A novel Monte Carlo technique. Implications on camphor ligand binding. J Chem Theory Comput 2005; 6: 1304-1311.
-
(2005)
J Chem Theory Comput
, vol.6
, pp. 1304-1311
-
-
Borrelli, K.W.1
Vitalis, A.2
Alcantara, R.3
Guallar, V.4
-
9
-
-
34250882254
-
pyDock: electrostatics and desolvation for effective scoring of rigid-body protein-protein docking
-
Cheng TM, Blundell TL, Fernandez-Recio J. pyDock: electrostatics and desolvation for effective scoring of rigid-body protein-protein docking. Proteins: Struct Funct Bioinform 2007; 68: 503-515.
-
(2007)
Proteins: Struct Funct Bioinform
, vol.68
, pp. 503-515
-
-
Cheng, T.M.1
Blundell, T.L.2
Fernandez-Recio, J.3
-
10
-
-
77949382951
-
Present and future challenges and limitations in protein-protein docking
-
Pons C, Grosdidier S, Solernou A, Pérez-Cano L, Fernández-Recio J. Present and future challenges and limitations in protein-protein docking. Proteins 2010; 78: 95-108.
-
(2010)
Proteins
, vol.78
, pp. 95-108
-
-
Pons, C.1
Grosdidier, S.2
Solernou, A.3
Pérez-Cano, L.4
Fernández-Recio, J.5
-
11
-
-
38549097715
-
Energy minimization in low-frequency normal modes to efficiently allow for global flexibility during systematic protein-protein docking
-
May A, Zacharias M. Energy minimization in low-frequency normal modes to efficiently allow for global flexibility during systematic protein-protein docking. Proteins 2008; 70: 794-809.
-
(2008)
Proteins
, vol.70
, pp. 794-809
-
-
May, A.1
Zacharias, M.2
-
12
-
-
48249138715
-
How to efficiently include receptor flexibility during computational docking
-
May A, Sieker F, Zacharias M. How to efficiently include receptor flexibility during computational docking. Curr Comput Aided Drug Des 2008; 4: 143-153.
-
(2008)
Curr Comput Aided Drug Des
, vol.4
, pp. 143-153
-
-
May, A.1
Sieker, F.2
Zacharias, M.3
-
13
-
-
42449161827
-
The interface of protein-protein complexes: analysis of contacts and prediction of interactions
-
Bahadur RP, Zacharias M. The interface of protein-protein complexes: analysis of contacts and prediction of interactions. Cellul Mol Life Sci 2008; 65: 1059-1072.
-
(2008)
Cellul Mol Life Sci
, vol.65
, pp. 1059-1072
-
-
Bahadur, R.P.1
Zacharias, M.2
-
14
-
-
34548861782
-
Protein-protein docking with backbone flexibility
-
Wang C, Bradley P, Baker D. Protein-protein docking with backbone flexibility. J Mol Biol 2007; 373: 503-519.
-
(2007)
J Mol Biol
, vol.373
, pp. 503-519
-
-
Wang, C.1
Bradley, P.2
Baker, D.3
-
15
-
-
0031565730
-
Modelling protein docking using shape complementarity, electrostatics, and biochemical information
-
Gabb HA, Jackson RM, Sternberg MJE. 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.E.3
-
16
-
-
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
-
17
-
-
77957944014
-
Protein-protein docking benchmark version 4.0
-
Hwang H, Vreven T, Janin J, Weng Z. Protein-protein docking benchmark version 4.0. Proteins 2010; 78: 3111-3114.
-
(2010)
Proteins
, vol.78
, pp. 3111-3114
-
-
Hwang, H.1
Vreven, T.2
Janin, J.3
Weng, Z.4
-
18
-
-
0036310711
-
On the role of crystal packing forces in determining protein sidechain conformations
-
Jacobson MP, Friesner RA, Xiang Z, Honig B. On the role of crystal packing forces in determining protein sidechain conformations. J Mol Biol 2002; 320: 597-608.
-
(2002)
J Mol Biol
, vol.320
, pp. 597-608
-
-
Jacobson, M.P.1
Friesner, R.A.2
Xiang, Z.3
Honig, B.4
-
19
-
-
1842532008
-
A hierarchical approach to all-atom loop prediction
-
Jacobson MP, Pincus DL, Rapp CS, Day TJF, Honig B, Shaw DE, Friesner RA. A hierarchical approach to all-atom loop prediction. Proteins 2004; 55: 351-367.
-
(2004)
Proteins
, vol.55
, pp. 351-367
-
-
Jacobson, M.P.1
Pincus, D.L.2
Rapp, C.S.3
Day, T.J.F.4
Honig, B.5
Shaw, D.E.6
Friesner, R.A.7
-
20
-
-
33847034125
-
Assignment of polar states for protein amino acid residues using an interaction cluster decomposition algorithm and its application to high resolution protein structure modeling
-
Li X, Jacobson MP, Zhu K, Zhao S, Friesner RA. Assignment of polar states for protein amino acid residues using an interaction cluster decomposition algorithm and its application to high resolution protein structure modeling. Proteins Struct Funct Bioinform 2007; 66: 824-837.
-
(2007)
Proteins Struct Funct Bioinform
, vol.66
, pp. 824-837
-
-
Li, X.1
Jacobson, M.P.2
Zhu, K.3
Zhao, S.4
Friesner, R.A.5
-
21
-
-
2942597884
-
First-shell solvation of ion pairs: correction of systematic errors in implicit solvent models
-
Yu Z, Jacobson MP, Josovitz J, Rapp CS, Friesner RA. First-shell solvation of ion pairs: correction of systematic errors in implicit solvent models. J Phys Chem B 2004; 108: 6643-6654.
-
(2004)
J Phys Chem B
, vol.108
, pp. 6643-6654
-
-
Yu, Z.1
Jacobson, M.P.2
Josovitz, J.3
Rapp, C.S.4
Friesner, R.A.5
-
22
-
-
0030955263
-
Understanding the recognition of protein structural classes by amino acid composition
-
Bahar I, Atilgan AR, Jernigan RL, Erman B. Understanding the recognition of protein structural classes by amino acid composition. Proteins 1997; 29: 172-185.
-
(1997)
Proteins
, vol.29
, pp. 172-185
-
-
Bahar, I.1
Atilgan, A.R.2
Jernigan, R.L.3
Erman, B.4
-
23
-
-
45749139232
-
Protein ligand docking accounting for receptor side chain and global flexibility in normal modes: evaluation on kinase inhibitor cross docking
-
May A, Zacharias M. Protein ligand docking accounting for receptor side chain and global flexibility in normal modes: evaluation on kinase inhibitor cross docking. J Med Chem 2008; 51: 3499-3506.
-
(2008)
J Med Chem
, vol.51
, pp. 3499-3506
-
-
May, A.1
Zacharias, M.2
-
24
-
-
0035044995
-
Conformational change of proteins arising from normal mode calculations
-
Tama F, Sanejouand H. Conformational change of proteins arising from normal mode calculations. Protein Eng 2001; 14: 1-6.
-
(2001)
Protein Eng
, vol.14
, pp. 1-6
-
-
Tama, F.1
Sanejouand, H.2
|