-
1
-
-
0036468396
-
Protein-protein association kinetics and protein docking
-
Camacho CJ, Vajda S. Protein-protein association kinetics and protein docking. Curr Opin Struct Biol 2002;12:36-40.
-
(2002)
Curr Opin Struct Biol
, vol.12
, pp. 36-40
-
-
Camacho, C.J.1
Vajda, S.2
-
2
-
-
0036468385
-
Prediction of protein-protein interactions by docking methods
-
Smith GR, Sternberg MJE. Prediction of protein-protein interactions by docking methods. Curr Opin Struct Biol 2002;12:28-35.
-
(2002)
Curr Opin Struct Biol
, vol.12
, pp. 28-35
-
-
Smith, G.R.1
Sternberg, M.J.E.2
-
3
-
-
0034663658
-
Scoring docked conformations generated by rigid-body protein-protein docking
-
Camacho CJ, Gatchell DW, Kimura SR, Vajda S. Scoring docked conformations generated by rigid-body protein-protein docking. Proteins 2000;40:525-537.
-
(2000)
Proteins
, vol.40
, pp. 525-537
-
-
Camacho, C.J.1
Gatchell, D.W.2
Kimura, S.R.3
Vajda, S.4
-
4
-
-
0031552370
-
Determination of atomic desolvation energies from the structures of crystallized proteins
-
Zhang C, Vasmatzis G, Cornette JL. Determination of atomic desolvation energies from the structures of crystallized proteins. J Mol Biol 1997;267:707-726.
-
(1997)
J Mol Biol
, vol.267
, pp. 707-726
-
-
Zhang, C.1
Vasmatzis, G.2
Cornette, J.L.3
-
5
-
-
0029421048
-
Protein-protein recognition
-
Janin J. Protein-protein recognition. Prog Biophys Mol Biol 1995;64:145-166.
-
(1995)
Prog Biophys Mol Biol
, vol.64
, pp. 145-166
-
-
Janin, J.1
-
7
-
-
0003187567
-
The atomic structure of protein-protein recognition sites
-
LoConte L, Chothia C, Janin J. The atomic structure of protein-protein recognition sites. J Mol Biol 1998;285:2177-2198.
-
(1998)
J Mol Biol
, vol.285
, pp. 2177-2198
-
-
LoConte, L.1
Chothia, C.2
Janin, J.3
-
8
-
-
0033566576
-
Examination of shape complementarity in docking of unbound proteins
-
Norel R, Petrey D, Wolfson HJ, Nussinov R. Examination of shape complementarity in docking of unbound proteins. Proteins 1999;36:307-317.
-
(1999)
Proteins
, vol.36
, pp. 307-317
-
-
Norel, R.1
Petrey, D.2
Wolfson, H.J.3
Nussinov, R.4
-
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
-
-
0030248996
-
Low-resolution docking: Prediction of complexes for undetermined structures
-
Vakser IA. Low-resolution docking: Prediction of complexes for undetermined structures. Biopolymers 1996;39:455-464.
-
(1996)
Biopolymers
, vol.39
, pp. 455-464
-
-
Vakser, I.A.1
-
11
-
-
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 U S A 1999;96:8477-8482.
-
(1999)
Proc Natl Acad Sci U S A
, vol.96
, pp. 8477-8482
-
-
Vakser, I.A.1
Matar, O.G.2
Lam, C.F.3
-
12
-
-
0033562633
-
Use of pair potentials across protein interfaces in screening predicted docked complexes
-
Moont G, Gabb HA, Sternberg MJE. Use of pair potentials across protein interfaces in screening predicted docked complexes. Proteins 1999;35:364-373.
-
(1999)
Proteins
, vol.35
, pp. 364-373
-
-
Moont, G.1
Gabb, H.A.2
Sternberg, M.J.E.3
-
13
-
-
0033081069
-
Protein-protein recognition: Exploring the energy funnels near the binding sites
-
Zhang C, Chan J, DeLisi C. Protein-protein recognition: Exploring the energy funnels near the binding sites. Proteins 1999;34:255-267.
-
(1999)
Proteins
, vol.34
, pp. 255-267
-
-
Zhang, C.1
Chan, J.2
DeLisi, C.3
-
14
-
-
0030968991
-
Empirical potentials and functions for protein folding and binding
-
Vajda S, Sippl M, Novotny J. Empirical potentials and functions for protein folding and binding. Curr Opin Struct Biol 1997;7:222-228.
-
(1997)
Curr Opin Struct Biol
, vol.7
, pp. 222-228
-
-
Vajda, S.1
Sippl, M.2
Novotny, J.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
-
-
0034575775
-
Protein-protein docking: Generation and filtering of complexes
-
Sternberg MJE, Gabb HA, Jackson, RM, Moont G. Protein-protein docking: Generation and filtering of complexes. Methods Mol Biol 2000;143:399-415.
-
(2000)
Methods Mol Biol
, vol.143
, pp. 399-415
-
-
Sternberg, M.J.E.1
Gabb, H.A.2
Jackson, R.M.3
Moont, G.4
-
17
-
-
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
-
18
-
-
33845377127
-
Estimation of effective interresidue contact energies from protein crystal structures: Quasi-chemical approximation
-
Miyazawa S, Jernigan RL. Estimation of effective interresidue contact energies from protein crystal structures: Quasi-chemical approximation. Macromolecules 1985;18:534-552.
-
(1985)
Macromolecules
, vol.18
, pp. 534-552
-
-
Miyazawa, S.1
Jernigan, R.L.2
-
19
-
-
0029919190
-
Residue-residue potentials with a favorable contact pair term and unfavorable high packing density terms, for simulation and threading
-
Miyazawa S, Jernigan RL. Residue-residue potentials with a favorable contact pair term and unfavorable high packing density terms, for simulation and threading. J Mol Biol 1996;256:623-644.
-
(1996)
J Mol Biol
, vol.256
, pp. 623-644
-
-
Miyazawa, S.1
Jernigan, R.L.2
-
20
-
-
0012227656
-
A comprehensive analytical treatment of continuum electrostatics
-
Schaefer M, Karplus M. A comprehensive analytical treatment of continuum electrostatics. J Phys Chem 1996;100:1578-1599.
-
(1996)
J Phys Chem
, vol.100
, pp. 1578-1599
-
-
Schaefer, M.1
Karplus, M.2
-
21
-
-
0028102849
-
The effect of conformational flexibility and solvation on receptor-ligand binding free energies
-
Vajda S, Weng Z, Rosenfeld R, DeLisi C. The effect of conformational flexibility and solvation on receptor-ligand binding free energies. Biochemistry 1994;33:13977-13987.
-
(1994)
Biochemistry
, vol.33
, pp. 13977-13987
-
-
Vajda, S.1
Weng, Z.2
Rosenfeld, R.3
DeLisi, C.4
-
22
-
-
0029933286
-
Prediction of protein complexes using empirical free energy functions
-
Weng Z, Vajda S, DeLisi C. Prediction of protein complexes using empirical free energy functions. Protein Sci 1996;5:614-626.
-
(1996)
Protein Sci
, vol.5
, pp. 614-626
-
-
Weng, Z.1
Vajda, S.2
DeLisi, C.3
-
23
-
-
84986512474
-
CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
-
Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem 1983;4:187-217.
-
(1983)
J Comput Chem
, vol.4
, pp. 187-217
-
-
Brooks, B.R.1
Bruccoleri, R.E.2
Olafson, B.D.3
States, D.J.4
Swaminathan, S.5
Karplus, M.6
-
24
-
-
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
-
26
-
-
0037093640
-
Welcome to CAPRI: A critical assessment of predicted interactions
-
Janin J. Welcome to CAPRI: A critical assessment of predicted interactions. Proteins 2002;47:257.
-
(2002)
Proteins
, vol.47
, pp. 257
-
-
Janin, J.1
-
27
-
-
0033776245
-
Docking structures of domains into maps from cryo-electron microscopy using local correlation
-
Roseman AM. Docking structures of domains into maps from cryo-electron microscopy using local correlation. Acta Crystallogr D 2000;56:1332-1340.
-
(2000)
Acta Crystallogr D
, vol.56
, pp. 1332-1340
-
-
Roseman, A.M.1
-
28
-
-
0034802465
-
Modeling tricks and fitting techniques for multi-resolution structures
-
Wriggers W, Chacon P. Modeling tricks and fitting techniques for multi-resolution structures. Structure 2001;9:779-788.
-
(2001)
Structure
, vol.9
, pp. 779-788
-
-
Wriggers, W.1
Chacon, P.2
-
29
-
-
0035845563
-
Protein docking along smooth association pathways
-
Camacho CJ, Vajda S. Protein docking along smooth association pathways. Proc Natl Acad Sci U S A 2001;98:10636-10641.
-
(2001)
Proc Natl Acad Sci U S A
, vol.98
, pp. 10636-10641
-
-
Camacho, C.J.1
Vajda, S.2
-
30
-
-
0035141353
-
Dynamical view of the positions of key side chains in protein-protein recognition
-
Kimura SR, Brower R, Vajda S, Camacho CJ. Dynamical view of the positions of key side chains in protein-protein recognition. Biophys J 2001;80:635-642.
-
(2001)
Biophys J
, vol.80
, pp. 635-642
-
-
Kimura, S.R.1
Brower, R.2
Vajda, S.3
Camacho, C.J.4
|