-
1
-
-
2942582560
-
A structural perspective on protein-protein interactions
-
Russell RB, Alber F, Aloy P, Davis FP, Korkin D, Pichaud M, Topf M, Sali A. A structural perspective on protein-protein interactions. Curr Opin Struct Biol 2004;14:313-324.
-
(2004)
Curr Opin Struct Biol
, vol.14
, pp. 313-324
-
-
Russell, R.B.1
Alber, F.2
Aloy, P.3
Davis, F.P.4
Korkin, D.5
Pichaud, M.6
Topf, M.7
Sali, A.8
-
2
-
-
0036606483
-
Principles of docking: An overview of search algorithms and a guide to scoring functions
-
Halperin I, Ma B, Wolfson H, Nussinov R. Principles of docking: An overview of search algorithms and a guide to scoring functions. Proteins 2002;47:409-443.
-
(2002)
Proteins
, vol.47
, pp. 409-443
-
-
Halperin, I.1
Ma, B.2
Wolfson, H.3
Nussinov, R.4
-
3
-
-
21644487998
-
The targets of CAPRI rounds 3-5
-
Janin J. The targets of CAPRI rounds 3-5. Proteins 2005;60:170-175.
-
(2005)
Proteins
, vol.60
, pp. 170-175
-
-
Janin, J.1
-
4
-
-
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
-
5
-
-
0037442962
-
HADDOCK: A protein-protein docking approach based on biochemical or biophysical information
-
Dominguez C, Boelens R, Bonvin AM. HADDOCK: a protein-protein docking approach based on biochemical 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.3
-
6
-
-
21644454184
-
Data-driven docking: HADDOCK'S adventures in CAPRI
-
van Dijk AD, de Vries SJ, Dominguez C, Chen H, Zhou HX, Bonvin AM. Data-driven docking: HADDOCK'S adventures in CAPRI. Proteins 2005;60:232-238.
-
(2005)
Proteins
, vol.60
, pp. 232-238
-
-
Van Dijk, A.D.1
De Vries, S.J.2
Dominguez, C.3
Chen, H.4
Zhou, H.X.5
Bonvin, A.M.6
-
7
-
-
12544256528
-
Data-driven docking for the study of biomolecular complexes
-
van Dijk ADJ, Boelens R, Bonvin AMJJ. Data-driven docking for the study of biomolecular complexes. FEBS J 2005;272:293-312.
-
(2005)
FEBS J
, vol.272
, pp. 293-312
-
-
Van Dijk, A.D.J.1
Boelens, R.2
Bonvin, A.3
-
8
-
-
0001895697
-
Evolutionary divergence and convergence in proteins
-
Bryson V, Vogel HJ, editors. New York: Academic Press
-
Zuckerkandl E, Pauling L. Evolutionary divergence and convergence in proteins. In: Bryson V, Vogel HJ, editors. Evolving genes and proteins. New York: Academic Press; 1965. p 97-166.
-
(1965)
Evolving Genes and Proteins
, pp. 97-166
-
-
Zuckerkandl, E.1
Pauling, L.2
-
9
-
-
2942741244
-
Evolutionary epitopes of Hsp90 and p23: Implications for their interaction
-
Zhu S, Tytgat J. Evolutionary epitopes of Hsp90 and p23: implications for their interaction. FASEB J 2004;18:940-947.
-
(2004)
FASEB J
, vol.18
, pp. 940-947
-
-
Zhu, S.1
Tytgat, J.2
-
10
-
-
0029664921
-
Evolutionarily conserved G(alpha beta gamma) binding surfaces support a model of the G protein-receptor complex
-
Lichtarge O, Bourne HR, Cohen FE. Evolutionarily conserved G(alpha beta gamma) binding surfaces support a model of the G protein-receptor complex. Proc Natl Acad Sci USA 1996;93:7507-7511.
-
(1996)
Proc Natl Acad Sci USA
, vol.93
, pp. 7507-7511
-
-
Lichtarge, O.1
Bourne, H.R.2
Cohen, F.E.3
-
11
-
-
0030821675
-
Correlated mutations contain information about protein-protein interaction
-
Pazos F, HelmerCitterich M, Ausiello G, Valencia A. Correlated mutations contain information about protein-protein interaction. J Mol Biol 1997;271:511-523.
-
(1997)
J Mol Biol
, vol.271
, pp. 511-523
-
-
Pazos, F.1
Helmercitterich, M.2
Ausiello, G.3
Valencia, A.4
-
12
-
-
0037296380
-
Phage-display and correlated mutations identify an essential region of subdomain 1C involved in homodimerization of Escherichia coli FtsA
-
Carettoni D, Gomez-Puertas P, Yim L, Mingorance J, Massidda O, Vicente M, Valencia A, Domenici E, Anderluzzi D. Phage-display and correlated mutations identify an essential region of subdomain 1C involved in homodimerization of Escherichia coli FtsA. Proteins Struct Funct Genet 2003;50:192-206.
-
(2003)
Proteins Struct Funct Genet
, vol.50
, pp. 192-206
-
-
Carettoni, D.1
Gomez-Puertas, P.2
Yim, L.3
Mingorance, J.4
Massidda, O.5
Vicente, M.6
Valencia, A.7
Domenici, E.8
Anderluzzi, D.9
-
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
-
-
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
-
15
-
-
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
-
16
-
-
0029913807
-
An evolutionary trace method defines binding surfaces common to protein families
-
Lichtarge O, Bourne HR, Cohen FE. An evolutionary trace method defines binding surfaces common to protein families. J Mol Biol 1996;257:342-358.
-
(1996)
J Mol Biol
, vol.257
, pp. 342-358
-
-
Lichtarge, O.1
Bourne, H.R.2
Cohen, F.E.3
-
17
-
-
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
-
18
-
-
0035896024
-
ConSurf: An algorithmic tool for the identification of functional regions in proteins by surface mapping of phylogenetic information
-
Armon A, Graur D, Ben Tal N. ConSurf: an algorithmic tool for the identification of functional regions in proteins by surface mapping of phylogenetic information. J Mol Biol 2001;307:447-463.
-
(2001)
J Mol Biol
, vol.307
, pp. 447-463
-
-
Armon, A.1
Graur, D.2
Ben Tal, N.3
-
19
-
-
0002218484
-
Rate4Site: An algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues
-
Pupko T, Bell RE, Mayrose I, Glaser F, Ben Tal N. Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues. Bioinformatics 2002;18(Suppl 1):S71-S77.
-
(2002)
Bioinformatics
, vol.18
, Issue.SUPPL. 1
-
-
Pupko, T.1
Bell, R.E.2
Mayrose, I.3
Glaser, F.4
Ben Tal, N.5
-
20
-
-
0035853280
-
Three-dimensional cluster analysis identifies interfaces and functional residue clusters in proteins
-
Landgraf R, Xenarios I, Eisenberg D. Three-dimensional cluster analysis identifies interfaces and functional residue clusters in proteins. J Mol Biol 2001;307:1487-1502.
-
(2001)
J Mol Biol
, vol.307
, pp. 1487-1502
-
-
Landgraf, R.1
Xenarios, I.2
Eisenberg, D.3
-
21
-
-
0026030641
-
Database of homology-derived protein structures and the structural meaning of sequence alignment
-
Sander C, Schneider R. Database of homology-derived protein structures and the structural meaning of sequence alignment. Proteins 1991;9:56-68.
-
(1991)
Proteins
, vol.9
, pp. 56-68
-
-
Sander, C.1
Schneider, R.2
-
22
-
-
0035882570
-
Prediction of protein interaction sites from sequence profile and residue neighbor list
-
Zhou HX, 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
-
23
-
-
23044487169
-
Statistical analysis and prediction of protein-protein interfaces
-
Bordner AJ, Abagyan R. Statistical analysis and prediction of protein-protein interfaces. Proteins 2005;60:353-366.
-
(2005)
Proteins
, vol.60
, pp. 353-366
-
-
Bordner, A.J.1
Abagyan, R.2
-
24
-
-
17444372787
-
Improved prediction of protein-protein binding sites using a support vector machines approach
-
Bradford JR, Westhead DR. Improved prediction of protein-protein binding sites using a support vector machines approach. Bioinformatics 2005;21:1487-1494.
-
(2005)
Bioinformatics
, vol.21
, pp. 1487-1494
-
-
Bradford, J.R.1
Westhead, D.R.2
-
25
-
-
0000228203
-
A model of evolutionary change in proteins
-
Dayhoff MO, editor. Washington, DC: National Biomedical Research Foundation
-
Dayhoff MO, Schwartz RM, Orcutt BC. A model of evolutionary change in proteins. In: Dayhoff MO, editor. Atlas of protein sequence and structure, vol 5, suppl 3. Washington, DC: National Biomedical Research Foundation; 1978. p 345-352.
-
(1978)
Atlas of Protein Sequence and Structure, Vol 5, Suppl 3
, vol.5
, pp. 345-352
-
-
Dayhoff, M.O.1
Schwartz, R.M.2
Orcutt, B.C.3
-
26
-
-
0000122573
-
PHYLIP-phylogeny inference package
-
Felsenstein J. PHYLIP-phylogeny inference package. Cladistics 1989;5:164-166.
-
(1989)
Cladistics
, vol.5
, pp. 164-166
-
-
Felsenstein, J.1
-
27
-
-
0031565725
-
Analysis of protein-protein interaction sites using surface patches
-
Jones S, Thornton JM. Analysis of protein-protein interaction sites using surface patches. J Mol Biol 1997;272:133-143.
-
(1997)
J Mol Biol
, vol.272
, pp. 133-143
-
-
Jones, S.1
Thornton, J.M.2
-
28
-
-
0037609791
-
Protein-protein interactions: Structurally conserved residues distinguish between binding sites and exposed protein surfaces
-
Ma B, Elkayam T, Wolfson H, Nussinov R. Protein-protein interactions: structurally conserved residues distinguish between binding sites and exposed protein surfaces. Proc Natl Acad Sci USA 2003;100:5772-5777.
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 5772-5777
-
-
Ma, B.1
Elkayam, T.2
Wolfson, H.3
Nussinov, R.4
-
29
-
-
1842507022
-
A new, structurally nonredundant, diverse data set of protein-protein interfaces and its implications
-
Keskin O, Tsai CJ, Wolfson H, Nussinov R. A new, structurally nonredundant, diverse data set of protein-protein interfaces and its implications. Protein Sci 2004;13:1043-1055.
-
(2004)
Protein Sci
, vol.13
, pp. 1043-1055
-
-
Keskin, O.1
Tsai, C.J.2
Wolfson, H.3
Nussinov, R.4
-
31
-
-
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
-
32
-
-
0033954256
-
The Protein Data Bank
-
Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The Protein Data Bank. Nucleic Acids Res 2000;28:235-242.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
Bhat, T.N.5
Weissig, H.6
Shindyalov, I.N.7
Bourne, P.E.8
-
34
-
-
0028922586
-
LIGPLOT: A program to generate schematic diagrams of protein-ligand interactions
-
Wallace AC, Laskowski RA, Thornton JM. LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions. Protein Eng 1995;8:127-134.
-
(1995)
Protein Eng
, vol.8
, pp. 127-134
-
-
Wallace, A.C.1
Laskowski, R.A.2
Thornton, J.M.3
-
35
-
-
1542390499
-
Identification of protein-protein interaction sites from docking energy landscapes
-
Fernandez-Recio J, Totrov M, Abagyan R. Identification of protein-protein interaction sites from docking energy landscapes. J Mol Biol 2004;335:843-865.
-
(2004)
J Mol Biol
, vol.335
, pp. 843-865
-
-
Fernandez-Recio, J.1
Totrov, M.2
Abagyan, R.3
-
36
-
-
0027457620
-
Receiver-operating characteristic (ROC) plots: A fundamental evaluation tool in clinical medicine
-
Zweig MH, Campbell G. Receiver-operating characteristic (ROC) plots: a fundamental evaluation tool in clinical medicine. Clin Chem 1993;39:561-577.
-
(1993)
Clin Chem
, vol.39
, pp. 561-577
-
-
Zweig, M.H.1
Campbell, G.2
-
37
-
-
13244262600
-
Assessing predictions of protein-protein interaction: The CAPRI experiment
-
Janin J. Assessing predictions of protein-protein interaction: the CAPRI experiment. Protein Sci 2005;14:278-283.
-
(2005)
Protein Sci
, vol.14
, pp. 278-283
-
-
Janin, J.1
-
38
-
-
0042010066
-
Asymmetric mutation rates at enzyme-inhibitor interfaces: Implications for the protein-protein docking problem
-
Bradford JR, Westhead DR. Asymmetric mutation rates at enzyme-inhibitor interfaces: implications for the protein-protein docking problem. Protein Sci 2003;12:2099-2103.
-
(2003)
Protein Sci
, vol.12
, pp. 2099-2103
-
-
Bradford, J.R.1
Westhead, D.R.2
-
40
-
-
0036122073
-
Prediction of protein-protein interaction sites in heterocomplexes with neural networks
-
Fariselli P, Pazos F, Valencia A, Casadio R. Prediction of protein-protein interaction sites in heterocomplexes with neural networks. Eur J Biochem 2002;269:1356-1361.
-
(2002)
Eur J Biochem
, vol.269
, pp. 1356-1361
-
-
Fariselli, P.1
Pazos, F.2
Valencia, A.3
Casadio, R.4
|