-
1
-
-
2942544498
-
Protein interaction networks from yeast to human
-
Bork P, et al. (2004) Protein interaction networks from yeast to human. Curr Opin Struct Biol 14:292-299.
-
(2004)
Curr Opin Struct Biol
, vol.14
, pp. 292-299
-
-
Bork, P.1
-
2
-
-
33645453254
-
Global landscape of protein complexes in the yeast Saccharomyces cerevisiae
-
Krogan NJ, et al. (2006) Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 440:637-643.
-
(2006)
Nature
, vol.440
, pp. 637-643
-
-
Krogan, N.J.1
-
3
-
-
0025123333
-
The structure of protein-protein recognition sites
-
Janin J, Chothia C (1990) The structure of protein-protein recognition sites. J Biol Chem 265:16027-16030.
-
(1990)
J Biol Chem
, vol.265
, pp. 16027-16030
-
-
Janin, J.1
Chothia, C.2
-
4
-
-
0030028728
-
Principles of protein-protein interactions
-
Jones S, Thornton JM (1996) Principles of protein-protein interactions. Proc Natl Acad Sci USA 93:13-20.
-
(1996)
Proc Natl Acad Sci USA
, vol.93
, pp. 13-20
-
-
Jones, S.1
Thornton, J.M.2
-
5
-
-
0031565729
-
Analysis of protein-protein interaction sites using surface patches
-
Jones S, Thornton JM (1997) Analysis of protein-protein interaction sites using surface patches. J Mol Biol 272:121-132.
-
(1997)
J Mol Biol
, vol.272
, pp. 121-132
-
-
Jones, S.1
Thornton, J.M.2
-
6
-
-
0003187567
-
The atomic structure of protein-protein recognition sites
-
Lo Conte L, Chothia C, Janin J (1999) The atomic structure of protein-protein recognition sites. J Mol Biol 285:2177-2198.
-
(1999)
J Mol Biol
, vol.285
, pp. 2177-2198
-
-
Lo Conte, L.1
Chothia, C.2
Janin, J.3
-
7
-
-
23044445176
-
Exploring the charge space of protein-protein association: A proteomic study
-
Shaul Y, Schreiber G (2005) Exploring the charge space of protein-protein association: a proteomic study. Proteins 60:341-352.
-
(2005)
Proteins
, vol.60
, pp. 341-352
-
-
Shaul, Y.1
Schreiber, G.2
-
8
-
-
0031565725
-
Prediction of protein-protein interaction sites using patch analysis
-
Jones S, Thornton JM (1997) Prediction of protein-protein interaction sites using patch analysis. J Mol Biol 272:133-143.
-
(1997)
J Mol Biol
, vol.272
, pp. 133-143
-
-
Jones, S.1
Thornton, J.M.2
-
9
-
-
0035882570
-
Prediction of protein interaction sites from sequence profile and residue neighbor list
-
Zhou HX, Shan Y (2001) Prediction of protein interaction sites from sequence profile and residue neighbor list. Proteins 44:336-343.
-
(2001)
Proteins
, vol.44
, pp. 336-343
-
-
Zhou, H.X.1
Shan, Y.2
-
10
-
-
0036122073
-
Prediction of protein-protein interaction sites in heterocomplexes with neural networks
-
Fariselli P, Pazos F, Valencia A, Casadio R (2002) Prediction of protein-protein interaction sites in heterocomplexes with neural networks. Eur J Biochem 269:1356-1361.
-
(2002)
Eur J Biochem
, vol.269
, pp. 1356-1361
-
-
Fariselli, P.1
Pazos, F.2
Valencia, A.3
Casadio, R.4
-
11
-
-
0038356582
-
Predicted protein-protein interaction sites from local sequence information
-
Ofran Y, Rost B (2003) Predicted protein-protein interaction sites from local sequence information. FEBS Lett 544:236-239.
-
(2003)
FEBS Lett
, vol.544
, pp. 236-239
-
-
Ofran, Y.1
Rost, B.2
-
12
-
-
1942422617
-
Pattern recognition strategies for molecular surfaces: III. Binding site prediction with a neural network
-
Keil M, Exner TE, Brickmann J (2004) Pattern recognition strategies for molecular surfaces: III. Binding site prediction with a neural network. J Comput Chem 25:779-789.
-
(2004)
J Comput Chem
, vol.25
, pp. 779-789
-
-
Keil, M.1
Exner, T.E.2
Brickmann, J.3
-
13
-
-
1842526090
-
ProMate: A structure based prediction program to identify the location of protein-protein binding sites
-
Neuvirth H, Raz R, Schreiber G (2004) ProMate: A structure based prediction program to identify the location of protein-protein binding sites. J Mol Biol 338:181-199.
-
(2004)
J Mol Biol
, vol.338
, pp. 181-199
-
-
Neuvirth, H.1
Raz, R.2
Schreiber, G.3
-
14
-
-
17444372787
-
Improved prediction of protein-protein binding sites using a support vector machines approach
-
Bradford JR, Westhead DR (2005) Improved prediction of protein-protein binding sites using a support vector machines approach. Bioinformatics 21:1487-1494.
-
(2005)
Bioinformatics
, vol.21
, pp. 1487-1494
-
-
Bradford, J.R.1
Westhead, D.R.2
-
15
-
-
0042386609
-
The relationship between sequence and interaction divergence in proteins
-
Aloy P, Ceulemans H, Stark A, Russell RB (2003) The relationship between sequence and interaction divergence in proteins. J Mol Biol 332:989-998.
-
(2003)
J Mol Biol
, vol.332
, pp. 989-998
-
-
Aloy, P.1
Ceulemans, H.2
Stark, A.3
Russell, R.B.4
-
16
-
-
28644448657
-
Survey of the geometric association of domain-domain interfaces
-
Kim WK, Ison JC (2005) Survey of the geometric association of domain-domain interfaces. Proteins 61:1075-1088.
-
(2005)
Proteins
, vol.61
, pp. 1075-1088
-
-
Kim, W.K.1
Ison, J.C.2
-
18
-
-
0029913807
-
An evolutionary trace method defines binding surfaces common to protein families
-
Lichtarge O, Bourne HR, Cohen FE (1996) An evolutionary trace method defines binding surfaces common to protein families. J Mol Biol 257:342-358.
-
(1996)
J Mol Biol
, vol.257
, pp. 342-358
-
-
Lichtarge, O.1
Bourne, H.R.2
Cohen, F.E.3
-
19
-
-
0035853280
-
Three-dimensional cluster analysis identifies interfaces and functional residue clusters in proteins
-
Landgraf R, Xenarios I, Eisenberg D (2001) Three-dimensional cluster analysis identifies interfaces and functional residue clusters in proteins. J Mol Biol 307:1487-1502.
-
(2001)
J Mol Biol
, vol.307
, pp. 1487-1502
-
-
Landgraf, R.1
Xenarios, I.2
Eisenberg, D.3
-
20
-
-
0002218484
-
Rate4Site: An algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues
-
Pupko T, et al. (2002) Rate4Site: An algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues. Bioinformatics 18 Suppl 1:S71-S77.
-
(2002)
Bioinformatics
, vol.18
, Issue.SUPPL. 1
-
-
Pupko, T.1
-
21
-
-
0346733329
-
Are protein-protein interfaces more conserved in sequence than the rest of the protein surface?
-
Caffrey DR, et al. (2004) Are protein-protein interfaces more conserved in sequence than the rest of the protein surface? Protein Sci 13:190-202.
-
(2004)
Protein Sci
, vol.13
, pp. 190-202
-
-
Caffrey, D.R.1
-
22
-
-
18844434719
-
Does structural and chemical divergence play a role in precluding undesirable protein interactions?
-
Jimenez JL (2005) Does structural and chemical divergence play a role in precluding undesirable protein interactions? Proteins 59:757-764.
-
(2005)
Proteins
, vol.59
, pp. 757-764
-
-
Jimenez, J.L.1
-
23
-
-
23344451687
-
Structure, function, and evolution of transient and obligate protein-protein interactions
-
Mintseris J, Weng Z (2005) Structure, function, and evolution of transient and obligate protein-protein interactions. Proc Natl Acad Sci USA 102:10930-10935.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 10930-10935
-
-
Mintseris, J.1
Weng, Z.2
-
24
-
-
13244277453
-
Physicochemical and residue conservation calculations to improve the ranking of protein-protein docking solutions
-
Duan Y, Reddy BV, Kaznessis YN (2005) Physicochemical and residue conservation calculations to improve the ranking of protein-protein docking solutions. Protein Sci 14:316-328.
-
(2005)
Protein Sci
, vol.14
, pp. 316-328
-
-
Duan, Y.1
Reddy, B.V.2
Kaznessis, Y.N.3
-
25
-
-
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 (2006) Efficient restraints for protein-protein docking by comparison of observed amino acid substitution patterns with those predicted from local environment. J Mol Biol 357:1669-1682.
-
(2006)
J Mol Biol
, vol.357
, pp. 1669-1682
-
-
Chelliah, V.1
Blundell, T.L.2
Fernandez-Recio, J.3
-
26
-
-
33646044395
-
WHISCY: What information does surface conservation yield? Application to data-driven docking
-
de Vries SJ, van Dijk AD, Bonvin AM (2006) WHISCY: What information does surface conservation yield? Application to data-driven docking. Proteins 63:479-489.
-
(2006)
Proteins
, vol.63
, pp. 479-489
-
-
de Vries, S.J.1
van Dijk, A.D.2
Bonvin, A.M.3
-
27
-
-
0028295169
-
Correlated mutations and residue contacts in proteins
-
Gobel U, Sander C, Schneider R, Valencia A (1994) Correlated mutations and residue contacts in proteins. Proteins 18:309-317.
-
(1994)
Proteins
, vol.18
, pp. 309-317
-
-
Gobel, U.1
Sander, C.2
Schneider, R.3
Valencia, A.4
-
28
-
-
0028125904
-
How frequent are correlated changes in families of protein sequences?
-
Neher E (1994) How frequent are correlated changes in families of protein sequences? Proc Natl Acad Sci USA 91:98-102.
-
(1994)
Proc Natl Acad Sci USA
, vol.91
, pp. 98-102
-
-
Neher, E.1
-
29
-
-
28444463255
-
Robust signals of coevolution of interacting residues in mammalian proteomes identified by phylogeny-aided structural analysis
-
Choi SS, Li W, Lahn BT (2005) Robust signals of coevolution of interacting residues in mammalian proteomes identified by phylogeny-aided structural analysis. Nat Genet 37:1367-1371.
-
(2005)
Nat Genet
, vol.37
, pp. 1367-1371
-
-
Choi, S.S.1
Li, W.2
Lahn, B.T.3
-
30
-
-
23944476399
-
A model-based approach for detecting coevolving positions in a molecule
-
Dutheil J, Pupko T, Jean-Marie A, Galtier N (2005) A model-based approach for detecting coevolving positions in a molecule. Mol Biol Evol 22:1919-1928.
-
(2005)
Mol Biol Evol
, vol.22
, pp. 1919-1928
-
-
Dutheil, J.1
Pupko, T.2
Jean-Marie, A.3
Galtier, N.4
-
31
-
-
0030821675
-
Correlated mutations contain information about protein-protein interaction
-
Pazos F, Helmer-Citterich M, Ausiello G, Valencia A (1997) Correlated mutations contain information about protein-protein interaction. J Mol Biol 271:511-523.
-
(1997)
J Mol Biol
, vol.271
, pp. 511-523
-
-
Pazos, F.1
Helmer-Citterich, M.2
Ausiello, G.3
Valencia, A.4
-
32
-
-
33646766064
-
Correlated mutations: Advances and limitations. A study on fusion proteins and on the Cohesin-Dockerin families
-
Halperin I, Wolfson H, Nussinov R (2006) Correlated mutations: advances and limitations. A study on fusion proteins and on the Cohesin-Dockerin families. Proteins 63:832-845.
-
(2006)
Proteins
, vol.63
, pp. 832-845
-
-
Halperin, I.1
Wolfson, H.2
Nussinov, R.3
-
33
-
-
33846925964
-
The molecular architecture of protein-protein binding sites
-
Reichmann D, et al. (2007) The molecular architecture of protein-protein binding sites. Curr Opin Struct Biol 17:67-76.
-
(2007)
Curr Opin Struct Biol
, vol.17
, pp. 67-76
-
-
Reichmann, D.1
-
34
-
-
2442646432
-
Large-scale co-evolution analysis of protein structural interlogues using the global protein structural interactome map (PSIMAP)
-
Kim WK, Bolser DM, Park JH (2004) Large-scale co-evolution analysis of protein structural interlogues using the global protein structural interactome map (PSIMAP). Bioinformatics 20:1138-1150.
-
(2004)
Bioinformatics
, vol.20
, pp. 1138-1150
-
-
Kim, W.K.1
Bolser, D.M.2
Park, J.H.3
-
35
-
-
0031565730
-
Modelling protein docking using shape complementarity, electrostatics and biochemical information
-
Gabb HA, Jackson RM, Sternberg MJ (1997) Modelling protein docking using shape complementarity, electrostatics and biochemical information. J Mol Biol 272:106-120.
-
(1997)
J Mol Biol
, vol.272
, pp. 106-120
-
-
Gabb, H.A.1
Jackson, R.M.2
Sternberg, M.J.3
-
36
-
-
4143051195
-
Comparison of site-specific rate-inference methods for protein sequences: Empirical Bayesian methods are superior
-
Mayrose I, Graur D, Ben-Tal N, Pupko T (2004) Comparison of site-specific rate-inference methods for protein sequences: Empirical Bayesian methods are superior. Mol Biol Evol 21:1781-1791.
-
(2004)
Mol Biol Evol
, vol.21
, pp. 1781-1791
-
-
Mayrose, I.1
Graur, D.2
Ben-Tal, N.3
Pupko, T.4
-
37
-
-
0035182669
-
Detection of conserved physicochemical characteristics of proteins by analyzing clusters of positions with co-ordinated substitutions
-
Afonnikov DA, Oshchepkov DY, Kolchanov NA (2001) Detection of conserved physicochemical characteristics of proteins by analyzing clusters of positions with co-ordinated substitutions. Bioinformatics 17:1035-1046.
-
(2001)
Bioinformatics
, vol.17
, pp. 1035-1046
-
-
Afonnikov, D.A.1
Oshchepkov, D.Y.2
Kolchanov, N.A.3
-
38
-
-
0033562633
-
Use of pair potentials across protein interfaces in screening predicted docked complexes
-
Moont G, Gabb HA, Sternberg MJ (1999) Use of pair potentials across protein interfaces in screening predicted docked complexes. Proteins 35:364-373.
-
(1999)
Proteins
, vol.35
, pp. 364-373
-
-
Moont, G.1
Gabb, H.A.2
Sternberg, M.J.3
-
39
-
-
0036306236
-
On the role of electrostatic interactions in the design of protein-protein interfaces
-
Sheinerman FB, Honig B (2002) On the role of electrostatic interactions in the design of protein-protein interfaces. J Mol Biol 318:161-177.
-
(2002)
J Mol Biol
, vol.318
, pp. 161-177
-
-
Sheinerman, F.B.1
Honig, B.2
-
40
-
-
33748261419
-
Electrostatic contribution to the binding stability of protein-protein complexes
-
Dong F, Zhou HX (2006) Electrostatic contribution to the binding stability of protein-protein complexes. Proteins 65:87-102.
-
(2006)
Proteins
, vol.65
, pp. 87-102
-
-
Dong, F.1
Zhou, H.X.2
-
41
-
-
34250882254
-
pyDock: Electrostatics and desolvation for effective scoring of rigid-body protein-protein docking
-
Man-Kuang Cheng T, Blundell TL, Fernandez-Recio J (2007) pyDock: Electrostatics and desolvation for effective scoring of rigid-body protein-protein docking. Proteins 68:503-515.
-
(2007)
Proteins
, vol.68
, pp. 503-515
-
-
Man-Kuang Cheng, T.1
Blundell, T.L.2
Fernandez-Recio, J.3
-
43
-
-
0242299207
-
Atomic contact vectors in protein-protein recognition
-
Mintseris J, Weng Z (2003) Atomic contact vectors in protein-protein recognition. Proteins 53:629-639.
-
(2003)
Proteins
, vol.53
, pp. 629-639
-
-
Mintseris, J.1
Weng, Z.2
-
44
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul SF, et al. (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res 25:3389-3402.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
-
45
-
-
0035177259
-
Similarity of phylogenetic trees as indicator of protein-protein interaction
-
Pazos F, Valencia A (2001) Similarity of phylogenetic trees as indicator of protein-protein interaction. Protein Eng 14:609-614.
-
(2001)
Protein Eng
, vol.14
, pp. 609-614
-
-
Pazos, F.1
Valencia, A.2
-
46
-
-
0026691182
-
The rapid generation of mutation data matrices from protein sequences
-
Jones DT, Taylor WR, Thornton JM (1992) The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci 8:275-282.
-
(1992)
Comput Appl Biosci
, vol.8
, pp. 275-282
-
-
Jones, D.T.1
Taylor, W.R.2
Thornton, J.M.3
-
48
-
-
0020475449
-
A simple method for displaying the hydropathic character of a protein
-
Kyte J, Doolittle RF (1982) A simple method for displaying the hydropathic character of a protein. J Mol Biol 157:105-132.
-
(1982)
J Mol Biol
, vol.157
, pp. 105-132
-
-
Kyte, J.1
Doolittle, R.F.2
-
49
-
-
0025398721
-
WHAT IF: A molecular modeling and drug design program
-
Vriend G (1990) WHAT IF: A molecular modeling and drug design program. J Mol Graphics 8:52-56, 29.
-
(1990)
J Mol Graphics
, vol.8
, Issue.52-56
, pp. 29
-
-
Vriend, G.1
|