-
2
-
-
0036601150
-
Computational methods for the prediction of protein interactions
-
Valencia A, Pazos F. Computational methods for the prediction of protein interactions. Curr Opin Struct Biol 2002;12:368-373.
-
(2002)
Curr Opin Struct Biol
, vol.12
, pp. 368-373
-
-
Valencia, A.1
Pazos, F.2
-
3
-
-
9244239761
-
A domain interaction map based on phylogenetic profiling
-
Pagel P, Wong P, Frishman D. A domain interaction map based on phylogenetic profiling. J Mol Biol 2004;344:1331-1346.
-
(2004)
J Mol Biol
, vol.344
, pp. 1331-1346
-
-
Pagel, P.1
Wong, P.2
Frishman, D.3
-
4
-
-
20144387067
-
The MIPS mammalian protein-protein interaction database
-
Pagel P, Kovac S, Oesterheld M, Brauner B, Dunger-Kaltenbach I, Frishman G, Montrone C, Mark P, Stümpflen V, Mewes HW, Ruepp A, Frishman D. The MIPS mammalian protein-protein interaction database. Bioinformatics 2005;21:832-834.
-
(2005)
Bioinformatics
, vol.21
, pp. 832-834
-
-
Pagel, P.1
Kovac, S.2
Oesterheld, M.3
Brauner, B.4
Dunger-Kaltenbach, I.5
Frishman, G.6
Montrone, C.7
Mark, P.8
Stümpflen, V.9
Mewes, H.W.10
Ruepp, A.11
Frishman, D.12
-
5
-
-
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
-
6
-
-
0038021436
-
Assessment of blind predictions of protein-protein interactions: Current status of docking methods
-
Méndez R, Leplae R, Maria LD, 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
-
-
Méndez, R.1
Leplae, R.2
Maria, L.D.3
Wodak, S.J.4
-
7
-
-
0036468385
-
Prediction of protein-protein interactions by docking methods
-
Smith GR, Sternberg MJ. 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.2
-
8
-
-
1242270553
-
Protein-protein docking: Is the glass half-full or half-empty?
-
Vajda S, Camacho CJ. Protein-protein docking: is the glass half-full or half-empty? Trends Biotechnol 2004;22:110-116.
-
(2004)
Trends Biotechnol
, vol.22
, pp. 110-116
-
-
Vajda, S.1
Camacho, C.J.2
-
9
-
-
1842861590
-
Prediction of protein-protein interactions: The CAPRI experiment, its evaluation and implications
-
Wodak SJ, Méndez R. Prediction of protein-protein interactions: the CAPRI experiment, its evaluation and implications. Curr Opin Struct Biol 2004;14:242-249.
-
(2004)
Curr Opin Struct Biol
, vol.14
, pp. 242-249
-
-
Wodak, S.J.1
Méndez, R.2
-
10
-
-
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
-
11
-
-
0036468670
-
Evolutionary predictions of binding surfaces and interactions
-
Lichtarge O, Sowa ME. Evolutionary predictions of binding surfaces and interactions. Curr Opin Struct Biol 2002;12:21-27.
-
(2002)
Curr Opin Struct Biol
, vol.12
, pp. 21-27
-
-
Lichtarge, O.1
Sowa, M.E.2
-
12
-
-
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
-
13
-
-
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
-
14
-
-
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
-
15
-
-
2542445427
-
ConSurf: Identification of functional regions in proteins by surface-mapping of phylogenetic information
-
Glaser F, Pupko T, Paz I, Bell RE, Bechor-Shental D, Martz E, Ben-Tal N. ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information. Bioinformatics 2003;19:163-164.
-
(2003)
Bioinformatics
, vol.19
, pp. 163-164
-
-
Glaser, F.1
Pupko, T.2
Paz, I.3
Bell, R.E.4
Bechor-Shental, D.5
Martz, E.6
Ben-Tal, N.7
-
16
-
-
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):71-77.
-
(2002)
Bioinformatics
, vol.18
, Issue.SUPPL. 1
, pp. 71-77
-
-
Pupko, T.1
Bell, R.E.2
Mayrose, I.3
Glaser, F.4
Ben-Tal, N.5
-
17
-
-
19544390737
-
REVCOM: A robust Bayesian method for evolutionary rate estimation
-
Bordner AJ, Abagyan R. REVCOM: a robust Bayesian method for evolutionary rate estimation. Bioinformatics 2005;21:2315-2321.
-
(2005)
Bioinformatics
, vol.21
, pp. 2315-2321
-
-
Bordner, A.J.1
Abagyan, R.2
-
18
-
-
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
-
19
-
-
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
-
20
-
-
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
-
21
-
-
1842765629
-
Prediction of protein-protein interaction sites using support vector machines
-
Koike A, Takagi T. Prediction of protein-protein interaction sites using support vector machines. Protein Eng Des Sel 2004;17:165-173.
-
(2004)
Protein Eng Des Sel
, vol.17
, pp. 165-173
-
-
Koike, A.1
Takagi, T.2
-
22
-
-
19944430515
-
Predicting binding sites of hydrolase-inhibitor complexes by combining several methods
-
Sen TZ, Kloczkowski A, Jernigan RL, Yan C, Honavar V, Ho KM, Wang CZ, Ihm Y, Cao H, Gu X, Dobbs D. Predicting binding sites of hydrolase-inhibitor complexes by combining several methods. BMC Bioinformatics 2004;5:205-205.
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 205-205
-
-
Sen, T.Z.1
Kloczkowski, A.2
Jernigan, R.L.3
Yan, C.4
Honavar, V.5
Ho, K.M.6
Wang, C.Z.7
Ihm, Y.8
Cao, H.9
Gu, X.10
Dobbs, D.11
-
23
-
-
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
-
24
-
-
0035914476
-
Conservation helps to identify biologically relevant crystal contacts
-
Valdar WS, Thornton JM. Conservation helps to identify biologically relevant crystal contacts. J Mol Biol 2001;313:399-416.
-
(2001)
J Mol Biol
, vol.313
, pp. 399-416
-
-
Valdar, W.S.1
Thornton, J.M.2
-
25
-
-
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
-
26
-
-
2942553723
-
Protein-protein interactions; coupling of structurally conserved residues and of hot spots across interfaces. Implications for docking
-
Halperin I, Wolfson H, Nussinov R. Protein-protein interactions; coupling of structurally conserved residues and of hot spots across interfaces. Implications for docking. Structure (Camb) 2004;12:1027-1038.
-
(2004)
Structure (Camb)
, vol.12
, pp. 1027-1038
-
-
Halperin, I.1
Wolfson, H.2
Nussinov, R.3
-
27
-
-
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
-
28
-
-
0037265213
-
Prediction of protein-protein interactions from evolutionary information
-
Valencia A, Pazos F. Prediction of protein-protein interactions from evolutionary information. Methods Biochem Anal 2003;44:411-426.
-
(2003)
Methods Biochem Anal
, vol.44
, pp. 411-426
-
-
Valencia, A.1
Pazos, F.2
-
29
-
-
0037197902
-
Interrogating protein interaction networks through structural biology
-
Aloy P, Russell RB. Interrogating protein interaction networks through structural biology. Proc Natl Acad Sci USA 2002;99:5896-5901.
-
(2002)
Proc Natl Acad Sci USA
, vol.99
, pp. 5896-5901
-
-
Aloy, P.1
Russell, R.B.2
-
30
-
-
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
-
31
-
-
0346733329
-
Are protein-protein interfaces more conserved in sequence than the rest of the protein surface?
-
Caffrey DR, Somaroo S, Hughes JD, Mintseris J, Huang ES. Are protein-protein interfaces more conserved in sequence than the rest of the protein surface? Protein Sci 2004;13:190-202.
-
(2004)
Protein Sci
, vol.13
, pp. 190-202
-
-
Caffrey, D.R.1
Somaroo, S.2
Hughes, J.D.3
Mintseris, J.4
Huang, E.S.5
-
32
-
-
23344451687
-
Structure, function, and evolution of transient and obligate protein-protein interactions
-
Mintseris J, Weng Z. Structure, function, and evolution of transient and obligate protein-protein interactions. Proc Natl Acad Sci USA 2005;102:10930-10935.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 10930-10935
-
-
Mintseris, J.1
Weng, Z.2
-
33
-
-
0029790856
-
Pitfalls of protein sequence analysis
-
Rost B, Valencia A. Pitfalls of protein sequence analysis. Curr Opin Biotechnol 1996;7:457-461.
-
(1996)
Curr Opin Biotechnol
, vol.7
, pp. 457-461
-
-
Rost, B.1
Valencia, A.2
-
34
-
-
0035815113
-
Evolution of function in protein superfamilies, from a structural perspective
-
Todd AE, Orengo CA, Thornton JM. Evolution of function in protein superfamilies, from a structural perspective. J Mol Biol 2001;307:1113-1143.
-
(2001)
J Mol Biol
, vol.307
, pp. 1113-1143
-
-
Todd, A.E.1
Orengo, C.A.2
Thornton, J.M.3
-
35
-
-
0029587166
-
A method to predict functional residues in proteins
-
Casari G, Sander C, Valencia A. A method to predict functional residues in proteins. Nat Struct Biol 1995;2:171-178.
-
(1995)
Nat Struct Biol
, vol.2
, pp. 171-178
-
-
Casari, G.1
Sander, C.2
Valencia, A.3
-
36
-
-
0037470597
-
Automatic methods for predicting functionally important residues
-
Mesa AdS, Pazos F, Valencia A. Automatic methods for predicting functionally important residues. J Mol Biol 2003;326:1289-1302.
-
(2003)
J Mol Biol
, vol.326
, pp. 1289-1302
-
-
Mesa, A.S.1
Pazos, F.2
Valencia, A.3
-
37
-
-
0036681416
-
Scoring residue conservation
-
Valdar WS. Scoring residue conservation. Proteins 2002;48:227-241.
-
(2002)
Proteins
, vol.48
, pp. 227-241
-
-
Valdar, W.S.1
-
38
-
-
1042275583
-
A dissection of specific and non-specific protein-protein interfaces
-
Bahadur RP, Chakrabarti P, Rodier F, Janin J. A dissection of specific and non-specific protein-protein interfaces. J Mol Biol 2004;336:943-955.
-
(2004)
J Mol Biol
, vol.336
, pp. 943-955
-
-
Bahadur, R.P.1
Chakrabarti, P.2
Rodier, F.3
Janin, J.4
-
39
-
-
0031565729
-
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;272:121-132.
-
(1997)
J Mol Biol
, vol.272
, pp. 121-132
-
-
Jones, S.1
Thornton, J.M.2
-
41
-
-
0003187567
-
The atomic structure of protein-protein recognition sites
-
Conte LL, Chothia C, Janin J. The atomic structure of protein-protein recognition sites. J Mol Biol 1999;285:2177-2198.
-
(1999)
J Mol Biol
, vol.285
, pp. 2177-2198
-
-
Conte, L.L.1
Chothia, C.2
Janin, J.3
-
42
-
-
0030580057
-
Antibody-antigen interactions: Contact analysis and binding site topography
-
MacCallum RM, Martin AC, Thornton JM. Antibody-antigen interactions: contact analysis and binding site topography. J Mol Biol 1996;262:732-745.
-
(1996)
J Mol Biol
, vol.262
, pp. 732-745
-
-
MacCallum, R.M.1
Martin, A.C.2
Thornton, J.M.3
-
43
-
-
0037474541
-
Structural characterisation and functional significance of transient protein-protein interactions
-
Nooren IM, Thornton JM. Structural characterisation and functional significance of transient protein-protein interactions. J Mol Biol 2003;325:991-1018.
-
(2003)
J Mol Biol
, vol.325
, pp. 991-1018
-
-
Nooren, I.M.1
Thornton, J.M.2
-
44
-
-
0037229456
-
Analysing six types of protein-protein interfaces
-
Ofran Y, Rost B. Analysing six types of protein-protein interfaces. J Mol Biol 2003;325:377-387.
-
(2003)
J Mol Biol
, vol.325
, pp. 377-387
-
-
Ofran, Y.1
Rost, B.2
-
46
-
-
1842405464
-
Studies of protein-protein interfaces: A statistical analysis of the hydrophobic effect
-
Tsai CJ, Lin SL, Wolfson HJ, Nussinov R. Studies of protein-protein interfaces: a statistical analysis of the hydrophobic effect. Protein Sci 1997;6:53-64.
-
(1997)
Protein Sci
, vol.6
, pp. 53-64
-
-
Tsai, C.J.1
Lin, S.L.2
Wolfson, H.J.3
Nussinov, R.4
-
47
-
-
0028332007
-
A role for surface hydrophobicity in protein-protein recognition
-
Young L, Jernigan RL, Covell DG. A role for surface hydrophobicity in protein-protein recognition. Protein Sci 1994;3:717-729.
-
(1994)
Protein Sci
, vol.3
, pp. 717-729
-
-
Young, L.1
Jernigan, R.L.2
Covell, D.G.3
-
48
-
-
0030028728
-
Principles of protein-protein interactions
-
Jones S, Thornton JM. Principles of protein-protein interactions. Proc Natl Acad Sci USA 1996;93:13-20.
-
(1996)
Proc Natl Acad Sci USA
, vol.93
, pp. 13-20
-
-
Jones, S.1
Thornton, J.M.2
-
49
-
-
0041312697
-
Diversity of protein-protein interactions
-
Nooren IM, Thornton JM. Diversity of protein-protein interactions. EMBO J 2003;22:3486-3492.
-
(2003)
EMBO J
, vol.22
, pp. 3486-3492
-
-
Nooren, I.M.1
Thornton, J.M.2
-
50
-
-
0032479179
-
Anatomy of hot spots in protein interfaces
-
Bogan AA, Thorn KS. Anatomy of hot spots in protein interfaces. J Mol Biol 1998;280:1-9.
-
(1998)
J Mol Biol
, vol.280
, pp. 1-9
-
-
Bogan, A.A.1
Thorn, K.S.2
-
51
-
-
0028916599
-
A hot spot of binding energy in a hormone-receptor interface
-
Clackson T, Wells JA. A hot spot of binding energy in a hormone-receptor interface. Science 1995;267:383-386.
-
(1995)
Science
, vol.267
, pp. 383-386
-
-
Clackson, T.1
Wells, J.A.2
-
53
-
-
0031565725
-
Prediction of protein-protein interaction sites using patch analysis
-
Jones S, Thornton JM. Prediction of protein-protein interaction sites using patch analysis. J Mol Biol 1997;272:133-143.
-
(1997)
J Mol Biol
, vol.272
, pp. 133-143
-
-
Jones, S.1
Thornton, J.M.2
-
54
-
-
0034049350
-
Kinetics of desolvation-mediated protein-protein binding
-
Camacho CJ, Kimura SR, DeLisi C, Vajda S. Kinetics of desolvation-mediated protein-protein binding. Biophys J 2000;78:1094-1105.
-
(2000)
Biophys J
, vol.78
, pp. 1094-1105
-
-
Camacho, C.J.1
Kimura, S.R.2
DeLisi, C.3
Vajda, S.4
-
55
-
-
0038300317
-
Algorithms for computational solvent mapping of proteins
-
Kortvelyesi T, Dennis S, Silberstein M, Brown L, Vajda S. Algorithms for computational solvent mapping of proteins. Proteins 2003;51:340-351.
-
(2003)
Proteins
, vol.51
, pp. 340-351
-
-
Kortvelyesi, T.1
Dennis, S.2
Silberstein, M.3
Brown, L.4
Vajda, S.5
-
56
-
-
10844235653
-
Optimal docking area: A new method for predicting protein-protein interaction sites
-
Fernandez-Recio J, Totrov M, Skorodumov C, Abagyan R. Optimal docking area: a new method for predicting protein-protein interaction sites. Proteins 2005;58:134-143.
-
(2005)
Proteins
, vol.58
, pp. 134-143
-
-
Fernandez-Recio, J.1
Totrov, M.2
Skorodumov, C.3
Abagyan, R.4
-
57
-
-
1942422617
-
Pattern recognition strategies for molecular surfaces. III. Binding site prediction with a neural network
-
Keil M, Exner TE, Brickmann J. Pattern recognition strategies for molecular surfaces. III. Binding site prediction with a neural network. J Comput Chem 2004;25:779-789.
-
(2004)
J Comput Chem
, vol.25
, pp. 779-789
-
-
Keil, M.1
Exner, T.E.2
Brickmann, J.3
-
58
-
-
11144325691
-
Partial least squares regression: A tutorial
-
Geladi P, Kowalski B. Partial least squares regression: a tutorial. Anal Chim Acta 1986;185:1-17.
-
(1986)
Anal Chim Acta
, vol.185
, pp. 1-17
-
-
Geladi, P.1
Kowalski, B.2
-
59
-
-
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
-
60
-
-
0015866154
-
Environment and exposure to solvent of protein atoms: Lysozyme and insulin
-
Shrake A, Rupley JA. Environment and exposure to solvent of protein atoms: lysozyme and insulin. J Mol Biol 1973;79:351-357.
-
(1973)
J Mol Biol
, vol.79
, pp. 351-357
-
-
Shrake, A.1
Rupley, J.A.2
-
61
-
-
84986522918
-
ICM: A new method for structure modeling and design: applications to docking and structure prediction from the distorted native conformation
-
Abagyan RA, Totrov MM, Kuznetsov DA. ICM: a new method for structure modeling and design: applications to docking and structure prediction from the distorted native conformation. J Comput Chem 1994;15:488-506.
-
(1994)
J Comput Chem
, vol.15
, pp. 488-506
-
-
Abagyan, R.A.1
Totrov, M.M.2
Kuznetsov, D.A.3
-
62
-
-
0025183708
-
Basic local alignment search tool
-
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990;215:403-410.
-
(1990)
J Mol Biol
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
63
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997;25:3389-3402.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schäffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
64
-
-
13444273448
-
The universal protein resource (UniProt)
-
Database issue
-
Bairoch A, Apweiler R, Wu CH, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Natale DA, O'Donovan C, Redaschi N, Yeh LS. The universal protein resource (UniProt). Nucleic Acids Res 2005;33:154-159. Database issue.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 154-159
-
-
Bairoch, A.1
Apweiler, R.2
Wu, C.H.3
Barker, W.C.4
Boeckmann, B.5
Ferro, S.6
Gasteiger, E.7
Huang, H.8
Lopez, R.9
Magrane, M.10
Martin, M.J.11
Natale, D.A.12
O'Donovan, C.13
Redaschi, N.14
Yeh, L.S.15
-
65
-
-
0031576355
-
Do aligned sequences share the same fold?
-
Abagyan RA, Batalov S. Do aligned sequences share the same fold? J Mol Biol 1997;273:355-368.
-
(1997)
J Mol Biol
, vol.273
, pp. 355-368
-
-
Abagyan, R.A.1
Batalov, S.2
-
66
-
-
0014757386
-
A general method applicable to the search for similarities in the amino acid sequence of two proteins
-
Needleman SB, Wunsch CD. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol 1970;48:443-453.
-
(1970)
J Mol Biol
, vol.48
, pp. 443-453
-
-
Needleman, S.B.1
Wunsch, C.D.2
-
67
-
-
0026656815
-
Exhaustive matching of the entire protein sequence database
-
Gonnet GH, Cohen MA, Benner SA. Exhaustive matching of the entire protein sequence database. Science 1992;256:1443-1445.
-
(1992)
Science
, vol.256
, pp. 1443-1445
-
-
Gonnet, G.H.1
Cohen, M.A.2
Benner, S.A.3
-
68
-
-
33947367995
-
-
Abagyan R. ICM Manual v. 3.1. 2005.
-
Abagyan R. ICM Manual v. 3.1. 2005.
-
-
-
-
69
-
-
0037093645
-
Dissecting protein-protein recognition sites
-
Chakrabarti P, Janin J. Dissecting protein-protein recognition sites. Proteins 2002;47:334-343.
-
(2002)
Proteins
, vol.47
, pp. 334-343
-
-
Chakrabarti, P.1
Janin, J.2
-
70
-
-
0035342450
-
Residue frequencies and pairing preferences at protein-protein interfaces
-
Glaser F, Steinberg DM, Vakser IA, Ben-Tal N. Residue frequencies and pairing preferences at protein-protein interfaces. Proteins 2001;43:89-102.
-
(2001)
Proteins
, vol.43
, pp. 89-102
-
-
Glaser, F.1
Steinberg, D.M.2
Vakser, I.A.3
Ben-Tal, N.4
-
71
-
-
0035053587
-
Assessing the role of tryptophan residues in the binding site
-
Samanta U, Chakrabarti P. Assessing the role of tryptophan residues in the binding site. Protein Eng 2001;14:7-15.
-
(2001)
Protein Eng
, vol.14
, pp. 7-15
-
-
Samanta, U.1
Chakrabarti, P.2
-
72
-
-
0035841343
-
Characterization of aromatic-thiol π-type hydrogen bonding and phenylalanine-cysteine side chain interactions through ab initio calculations and protein database analyses
-
Duan G, Smith VHJ, Weaver DF. Characterization of aromatic-thiol π-type hydrogen bonding and phenylalanine-cysteine side chain interactions through ab initio calculations and protein database analyses. Mol Phys 2001;99:1689-1699.
-
(2001)
Mol Phys
, vol.99
, pp. 1689-1699
-
-
Duan, G.1
Smith, V.H.J.2
Weaver, D.F.3
-
73
-
-
0034846083
-
Non-hydrogen bond interactions involving the methionine sulfur atom
-
Pal D, Chakrabarti P. Non-hydrogen bond interactions involving the methionine sulfur atom. J Biomol Struct Dyn 2001;19:115-128.
-
(2001)
J Biomol Struct Dyn
, vol.19
, pp. 115-128
-
-
Pal, D.1
Chakrabarti, P.2
-
75
-
-
0031552370
-
Determination of atomic desolvation energies from the structures of crystallized proteins
-
Zhang C, Vasmatzis G, Cornette JL, DeLisi C. 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
DeLisi, C.4
-
76
-
-
0029918062
-
Crystal structure and mutational analysis of the human CDK2 kinase complex with cell cycle-regulatory protein CksHs1
-
Bourne Y, Watson MH, Hickey MJ, Holmes W, Rocque W, Reed SI, Tainer JA. Crystal structure and mutational analysis of the human CDK2 kinase complex with cell cycle-regulatory protein CksHs1. Cell 1996;84:863-874.
-
(1996)
Cell
, vol.84
, pp. 863-874
-
-
Bourne, Y.1
Watson, M.H.2
Hickey, M.J.3
Holmes, W.4
Rocque, W.5
Reed, S.I.6
Tainer, J.A.7
-
77
-
-
0029767016
-
Structural basis of cyclin-dependent kinase activation by phosphorylation
-
Russo AA, Jeffrey PD, Pavletich NP. Structural basis of cyclin-dependent kinase activation by phosphorylation. Nat Struct Biol 1996;3:696-700.
-
(1996)
Nat Struct Biol
, vol.3
, pp. 696-700
-
-
Russo, A.A.1
Jeffrey, P.D.2
Pavletich, N.P.3
-
78
-
-
0025998314
-
Multiple murine α 1-protease inhibitor genes show unusual evolutionary divergence
-
Borriello F, Krauter KS. Multiple murine α 1-protease inhibitor genes show unusual evolutionary divergence. Proc Natl Acad Sci USA 1991;88:9417-9421.
-
(1991)
Proc Natl Acad Sci USA
, vol.88
, pp. 9417-9421
-
-
Borriello, F.1
Krauter, K.S.2
-
79
-
-
0024382970
-
Functional evolutionary divergence of proteolytic enzymes and their inhibitors
-
Creighton TE, Darby NJ. Functional evolutionary divergence of proteolytic enzymes and their inhibitors. Trends Biochem Sci 1989;14:319-324.
-
(1989)
Trends Biochem Sci
, vol.14
, pp. 319-324
-
-
Creighton, T.E.1
Darby, N.J.2
-
80
-
-
0028140075
-
Evolution of murine α 1-proteinase inhibitors: Gene amplification and reactive center divergence
-
Rheaume C, Goodwin RL, Latimer JJ, Baumann H, Berger FG. Evolution of murine α 1-proteinase inhibitors: gene amplification and reactive center divergence. J Mol Evol 1994;38:121-131.
-
(1994)
J Mol Evol
, vol.38
, pp. 121-131
-
-
Rheaume, C.1
Goodwin, R.L.2
Latimer, J.J.3
Baumann, H.4
Berger, F.G.5
-
81
-
-
0030063088
-
Patterns of divergence during evolution of α 1-proteinase inhibitors in mammals
-
Goodwin RL, Baumann H, Berger FG. Patterns of divergence during evolution of α 1-proteinase inhibitors in mammals. Mol Biol Evol 1996;13:346-358.
-
(1996)
Mol Biol Evol
, vol.13
, pp. 346-358
-
-
Goodwin, R.L.1
Baumann, H.2
Berger, F.G.3
-
82
-
-
0023188637
-
Accelerated evolution in the reactive centre regions of serine protease inhibitors
-
Hill RE, Hastie ND. Accelerated evolution in the reactive centre regions of serine protease inhibitors. Nature 1987;326:96-99.
-
(1987)
Nature
, vol.326
, pp. 96-99
-
-
Hill, R.E.1
Hastie, N.D.2
-
83
-
-
21644469377
-
Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures
-
Méndez 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
-
-
Méndez, R.1
Leplae, R.2
Lensink, M.F.3
Wodak, S.J.4
-
84
-
-
0032169688
-
PQS: A protein quaternary structure file server
-
Henrick K, Thornton JM. PQS: a protein quaternary structure file server. Trends Biochem Sci 1998;23:358-361.
-
(1998)
Trends Biochem Sci
, vol.23
, pp. 358-361
-
-
Henrick, K.1
Thornton, J.M.2
-
85
-
-
0034308172
-
Discriminating between homodimeric and monomeric proteins in the crystalline state
-
Ponstingl H, Henrick K, Thornton JM. Discriminating between homodimeric and monomeric proteins in the crystalline state. Proteins 2000;41:47-57.
-
(2000)
Proteins
, vol.41
, pp. 47-57
-
-
Ponstingl, H.1
Henrick, K.2
Thornton, J.M.3
-
86
-
-
0031787909
-
Aminoacyl tRNA synthetases as targets for new anti-infectives
-
Schimmel P, Tao J, Hill J. Aminoacyl tRNA synthetases as targets for new anti-infectives. FASEB J 1998;12:1599-1609.
-
(1998)
FASEB J
, vol.12
, pp. 1599-1609
-
-
Schimmel, P.1
Tao, J.2
Hill, J.3
-
87
-
-
0034815817
-
Crystal structure of Staphylococcus aureus tyrosyl-tRNA synthetase in complex with a class of potent and specific inhibitors
-
Qiu X, Janson CA, Smith WW, Green SM, McDevitt P, Johanson K, Carter P, Hibbs M, Lewis C, Chalker A, Fosberry A, Lalonde J, Berge J, Brown P, Houge-Frydrych CS, Jarvest RL. Crystal structure of Staphylococcus aureus tyrosyl-tRNA synthetase in complex with a class of potent and specific inhibitors. Protein Sci 2001;10:2008-2016.
-
(2001)
Protein Sci
, vol.10
, pp. 2008-2016
-
-
Qiu, X.1
Janson, C.A.2
Smith, W.W.3
Green, S.M.4
McDevitt, P.5
Johanson, K.6
Carter, P.7
Hibbs, M.8
Lewis, C.9
Chalker, A.10
Fosberry, A.11
Lalonde, J.12
Berge, J.13
Brown, P.14
Houge-Frydrych, C.S.15
Jarvest, R.L.16
-
88
-
-
12344283963
-
Structural snapshots of the KMSKS loop rearrangement for amino acid activation by bacterial tyrosyl-tRNA synthetase
-
Kobayashi T, Takimura T, Sekine R, Vincent K, Kamata K, Sakamoto K, Nishimura S, Yokoyama S. Structural snapshots of the KMSKS loop rearrangement for amino acid activation by bacterial tyrosyl-tRNA synthetase. J Mol Biol 2005;346:105-117.
-
(2005)
J Mol Biol
, vol.346
, pp. 105-117
-
-
Kobayashi, T.1
Takimura, T.2
Sekine, R.3
Vincent, K.4
Kamata, K.5
Sakamoto, K.6
Nishimura, S.7
Yokoyama, S.8
-
89
-
-
0029911754
-
Swiveling-domain mechanism for enzymatic phosphotransfer between remote reaction sites
-
Herzberg O, Chen CC, Kapadia G, McGuire M, Carroll LJ, Noh SJ, Dunaway-Mariano D. Swiveling-domain mechanism for enzymatic phosphotransfer between remote reaction sites. Proc Natl Acad Sci USA 1996;93:2652-2657.
-
(1996)
Proc Natl Acad Sci USA
, vol.93
, pp. 2652-2657
-
-
Herzberg, O.1
Chen, C.C.2
Kapadia, G.3
McGuire, M.4
Carroll, L.J.5
Noh, S.J.6
Dunaway-Mariano, D.7
|