-
1
-
-
0034628508
-
A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae
-
Uetz P, Giot L, Cagney G, Mansfield TA, Judson RS, Knight JR, Lockshon D, Narayan V, Srinivasan M, Pochart P, Qureshi-Emili A, Li Y, Godwin B, Conover D, Kalbfleisch T, Vijayadamodar G, Yang M, Johnston M, Fields S, Rothberg JM. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 2000;403:623-627.
-
(2000)
Nature
, vol.403
, pp. 623-627
-
-
Uetz, P.1
Giot, L.2
Cagney, G.3
Mansfield, T.A.4
Judson, R.S.5
Knight, J.R.6
Lockshon, D.7
Narayan, V.8
Srinivasan, M.9
Pochart, P.10
Qureshi-Emili, A.11
Li, Y.12
Godwin, B.13
Conover, D.14
Kalbfleisch, T.15
Vijayadamodar, G.16
Yang, M.17
Johnston, M.18
Fields, S.19
Rothberg, J.M.20
more..
-
2
-
-
0037435030
-
Mass spectrometry-based proteomics
-
Aebersold R, Mann M. Mass spectrometry-based proteomics. Nature 2003;422:198-207.
-
(2003)
Nature
, vol.422
, pp. 198-207
-
-
Aebersold, R.1
Mann, M.2
-
3
-
-
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
-
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
-
-
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
-
-
0026310932
-
Soft docking: Matching of molecular surface cubes
-
Jiang F, Kim SH. "Soft docking": matching of molecular surface cubes. J Mol Biol 1991;219:79-102.
-
(1991)
J Mol Biol
, vol.219
, pp. 79-102
-
-
Jiang, F.1
Kim, S.H.2
-
7
-
-
0026572775
-
Molecular surface recognition: Determination of geometric fit between proteins and their ligands by correlation techniques
-
Katchalski-Katzir E, Shariv I, Eisenstein M, Friesem AA, Aflalo C, Vakser IA. Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques. Proc Natl Acad Sci USA 1992;89:2195-2199.
-
(1992)
Proc Natl Acad Sci USA
, vol.89
, pp. 2195-2199
-
-
Katchalski-Katzir, E.1
Shariv, I.2
Eisenstein, M.3
Friesem, A.A.4
Aflalo, C.5
Vakser, I.A.6
-
8
-
-
0026464639
-
New algorithm to model protein-protein recognition based on surface complementarity. Applications to antibody-antigen docking
-
Walls PH, Sternberg MJ. New algorithm to model protein-protein recognition based on surface complementarity. Applications to antibody-antigen docking. J Mol Biol 1992;228:277-297.
-
(1992)
J Mol Biol
, vol.228
, pp. 277-297
-
-
Walls, P.H.1
Sternberg, M.J.2
-
10
-
-
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
-
11
-
-
0003187567
-
The atomic structure of protein-protein recognition sites
-
Lo Conte L, 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
-
-
Lo Conte, L.1
Chothia, C.2
Janin, J.3
-
12
-
-
0030855390
-
ESCHER: A new docking procedure applied to the reconstruction of protein tertiary structure
-
Ausiello G, Cesareni G, Helmer-Citterich M. ESCHER: a new docking procedure applied to the reconstruction of protein tertiary structure. Proteins 1997;28:556-567.
-
(1997)
Proteins
, vol.28
, pp. 556-567
-
-
Ausiello, G.1
Cesareni, G.2
Helmer-Citterich, M.3
-
13
-
-
0031565730
-
Modelling protein docking using shape complementarity, electrostatics and biochemical information
-
Gabb HA, Jackson RM, Sternberg MJ. 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.3
-
14
-
-
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
-
15
-
-
0030598347
-
Hydrogen bonding and molecular surface shape complementarity as a basis for protein docking
-
Meyer M, Wilson P, Schomburg D. Hydrogen bonding and molecular surface shape complementarity as a basis for protein docking. J Mol Biol 1996;264:199-210.
-
(1996)
J Mol Biol
, vol.264
, pp. 199-210
-
-
Meyer, M.1
Wilson, P.2
Schomburg, D.3
-
16
-
-
0028575449
-
Hydrophobic docking: A proposed enhancement to molecular recognition techniques
-
Vakser IA, Aflalo C. Hydrophobic docking: a proposed enhancement to molecular recognition techniques. Proteins 1994;20:320-329.
-
(1994)
Proteins
, vol.20
, pp. 320-329
-
-
Vakser, I.A.1
Aflalo, C.2
-
17
-
-
0031704966
-
Estimation and filtering of potential protein-protein docking positions
-
Ackermann F, Herrmann G, Posch S, Sagerer G. Estimation and filtering of potential protein-protein docking positions. Bioinformatics 1998;14:196-205.
-
(1998)
Bioinformatics
, vol.14
, pp. 196-205
-
-
Ackermann, F.1
Herrmann, G.2
Posch, S.3
Sagerer, G.4
-
18
-
-
0032515101
-
A soft, mean-field potential derived from crystal contacts for predicting protein-protein interactions
-
Robert CH, Janin J. A soft, mean-field potential derived from crystal contacts for predicting protein-protein interactions. J Mol Biol 1998;283:1037-1047.
-
(1998)
J Mol Biol
, vol.283
, pp. 1037-1047
-
-
Robert, C.H.1
Janin, J.2
-
19
-
-
0033562633
-
Use of pair potentials across protein interfaces in screening predicted docked complexes
-
Moont G, Gabb HA, Sternberg MJ. 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.3
-
20
-
-
0038161052
-
Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations
-
Gray JJ, Moughon S, Wang C, Schueler-Furman O, Kuhlman B, Rohl CA, Baker D. Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. J Mol Biol 2003;331:281-299.
-
(2003)
J Mol Biol
, vol.331
, pp. 281-299
-
-
Gray, J.J.1
Moughon, S.2
Wang, C.3
Schueler-Furman, O.4
Kuhlman, B.5
Rohl, C.A.6
Baker, D.7
-
21
-
-
1642534609
-
An accurate, residue-level, pair potential of mean force for folding and binding based on the distance-scaled, ideal-gas reference state
-
Zhang C, Liu S, Zhou H, Zhou Y. An accurate, residue-level, pair potential of mean force for folding and binding based on the distance-scaled, ideal-gas reference state. Protein Sci 2004;13:400-411.
-
(2004)
Protein Sci
, vol.13
, pp. 400-411
-
-
Zhang, C.1
Liu, S.2
Zhou, H.3
Zhou, Y.4
-
22
-
-
17144383951
-
A knowledge-based energy function for protein-ligand, protein-protein, and protein-DNA complexes
-
Zhang C, Liu S, Zhu Q, Zhou Y. A knowledge-based energy function for protein-ligand, protein-protein, and protein-DNA complexes. J Med Chem 2005;48:2325-2335.
-
(2005)
J Med Chem
, vol.48
, pp. 2325-2335
-
-
Zhang, C.1
Liu, S.2
Zhu, Q.3
Zhou, Y.4
-
23
-
-
21644446565
-
Docking prediction using biological information, ZDOCK sampling technique, and clustering guided by the DFIRE statistical energy function
-
Zhang C, Liu S, Zhou Y. Docking prediction using biological information, ZDOCK sampling technique, and clustering guided by the DFIRE statistical energy function. Proteins 2005;60:314-318.
-
(2005)
Proteins
, vol.60
, pp. 314-318
-
-
Zhang, C.1
Liu, S.2
Zhou, Y.3
-
24
-
-
0025341310
-
Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins
-
Sippl MJ. Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins. J Mol Biol 1990;213:859-883.
-
(1990)
J Mol Biol
, vol.213
, pp. 859-883
-
-
Sippl, M.J.1
-
25
-
-
0026726481
-
Topology fingerprint approach to the inverse protein folding problem
-
Godzik A, Kolinski A, Skolnick J. Topology fingerprint approach to the inverse protein folding problem. J Mol Biol 1992;227:227-238.
-
(1992)
J Mol Biol
, vol.227
, pp. 227-238
-
-
Godzik, A.1
Kolinski, A.2
Skolnick, J.3
-
26
-
-
0026690571
-
A new approach to protein fold recognition
-
Jones DT, Taylor WR, Thornton JM. A new approach to protein fold recognition. Nature 1992;358:86-89.
-
(1992)
Nature
, vol.358
, pp. 86-89
-
-
Jones, D.T.1
Taylor, W.R.2
Thornton, J.M.3
-
27
-
-
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
-
28
-
-
0037068492
-
Drugscore meets CoMFA: Adaptation of fields for molecular comparison (AFMoC) or how to tailor knowledge-based pair-potentials to a particular protein
-
Gohlke H, Klebe G. Drugscore meets CoMFA: adaptation of fields for molecular comparison (AFMoC) or how to tailor knowledge-based pair-potentials to a particular protein. J Med Chem 2002;45:4153-4170.
-
(2002)
J Med Chem
, vol.45
, pp. 4153-4170
-
-
Gohlke, H.1
Klebe, G.2
-
29
-
-
23944499528
-
Improving binding mode predictions by docking into protein-specifically adapted potential fields
-
Radestock S, Bohm M, Gohlke H. Improving binding mode predictions by docking into protein-specifically adapted potential fields. J Med Chem 2005;48:5466-5479.
-
(2005)
J Med Chem
, vol.48
, pp. 5466-5479
-
-
Radestock, S.1
Bohm, M.2
Gohlke, H.3
-
30
-
-
0032939176
-
Solution structure of the 40,000 Mr phosphoryl transfer complex between the N-terminal domain of enzyme I and HPr
-
Garrett DS, Seok YJ, Peterkofsky A, Gronenborn AM, Clore GM. Solution structure of the 40,000 Mr phosphoryl transfer complex between the N-terminal domain of enzyme I and HPr. Nat Struct Biol 1999;6:166-173.
-
(1999)
Nat Struct Biol
, vol.6
, pp. 166-173
-
-
Garrett, D.S.1
Seok, Y.J.2
Peterkofsky, A.3
Gronenborn, A.M.4
Clore, G.M.5
-
31
-
-
0034329415
-
Solution structure of the phosphoryl transfer complex between the signal transducing proteins HPr and IIA(glucose) of the Escherichia coli phosphoenolpyruvate: Sugar phosphotransferase system
-
Wang G, Louis JM, Sondej M, Seok YJ, Peterkofsky A, Clore GM. Solution structure of the phosphoryl transfer complex between the signal transducing proteins HPr and IIA(glucose) of the Escherichia coli phosphoenolpyruvate: sugar phosphotransferase system. EMBO J 2000;19:5635-5649.
-
(2000)
EMBO J
, vol.19
, pp. 5635-5649
-
-
Wang, G.1
Louis, J.M.2
Sondej, M.3
Seok, Y.J.4
Peterkofsky, A.5
Clore, G.M.6
-
32
-
-
0036829797
-
Solution structure of the phosphoryl transfer complex between the cytoplasmic A domain of the mannitol transporter IIMannitol and HPr of the Escherichia coli phosphotransferase system
-
Cornilescu G, Lee BR, Cornilescu CC, Wang G, Peterkofsky A, Clore GM. Solution structure of the phosphoryl transfer complex between the cytoplasmic A domain of the mannitol transporter IIMannitol and HPr of the Escherichia coli phosphotransferase system. J Biol Chem 2002;277:42289-42298.
-
(2002)
J Biol Chem
, vol.277
, pp. 42289-42298
-
-
Cornilescu, G.1
Lee, B.R.2
Cornilescu, C.C.3
Wang, G.4
Peterkofsky, A.5
Clore, G.M.6
-
33
-
-
20144384787
-
Solution NMR structure of the 48-kDa IIAMannose-HPr complex of the Escherichia coli mannose phosphotransferase system
-
Williams DC, Jr, Cai M, Suh JY, Peterkofsky A, Clore GM. Solution NMR structure of the 48-kDa IIAMannose-HPr complex of the Escherichia coli mannose phosphotransferase system. J Biol Chem 2005;280:20775-20784.
-
(2005)
J Biol Chem
, vol.280
, pp. 20775-20784
-
-
Williams Jr, D.C.1
Cai, M.2
Suh, J.Y.3
Peterkofsky, A.4
Clore, G.M.5
-
34
-
-
33644772777
-
The transcription regulator RbsR represents a novel interaction partner of the phosphoprotein HPr-Ser46-P in Bacillus subtilis
-
Muller W, Horstmann N, Hillen W, Sticht H. The transcription regulator RbsR represents a novel interaction partner of the phosphoprotein HPr-Ser46-P in Bacillus subtilis. FEBS J 2006;273:1251-1261.
-
(2006)
FEBS J
, vol.273
, pp. 1251-1261
-
-
Muller, W.1
Horstmann, N.2
Hillen, W.3
Sticht, H.4
-
35
-
-
0034567210
-
Comparative protein structure modeling. Introduction and practical examples with modeller
-
Sanchez R, Sali A. Comparative protein structure modeling. Introduction and practical examples with modeller. Methods Mol Biol 2000;143:97-129.
-
(2000)
Methods Mol Biol
, vol.143
, pp. 97-129
-
-
Sanchez, R.1
Sali, A.2
-
36
-
-
0027340388
-
The 2.0-A resolution structure of Escherichia coli histidine-containing phosphocarrier protein HPr. A redetermination
-
Jia Z, Quail JW, Waygood EB, Delbaere LT. The 2.0-A resolution structure of Escherichia coli histidine-containing phosphocarrier protein HPr. A redetermination. J Biol Chem 1993;268:22490-22501.
-
(1993)
J Biol Chem
, vol.268
, pp. 22490-22501
-
-
Jia, Z.1
Quail, J.W.2
Waygood, E.B.3
Delbaere, L.T.4
-
37
-
-
0031019983
-
Solution structure of the 30 kDa N-terminal domain of enzyme I of the Escherichia coli phosphoenolpyruvate: Sugar phosphotransferase system by multidimensional NMR
-
Garrett DS, Seok YJ, Liao DI, Peterkofsky A, Gronenborn AM, Clore GM. Solution structure of the 30 kDa N-terminal domain of enzyme I of the Escherichia coli phosphoenolpyruvate: sugar phosphotransferase system by multidimensional NMR. Biochemistry 1997;36:2517-2530.
-
(1997)
Biochemistry
, vol.36
, pp. 2517-2530
-
-
Garrett, D.S.1
Seok, Y.J.2
Liao, D.I.3
Peterkofsky, A.4
Gronenborn, A.M.5
Clore, G.M.6
-
38
-
-
0031414754
-
Structural studies of the Escherichia coli signal transducing protein IIAGlc: Implications for target recognition
-
Feese MD, Comolli L, Meadow ND, Roseman S, Remington SJ. Structural studies of the Escherichia coli signal transducing protein IIAGlc: implications for target recognition. Biochemistry 1997;36:16087-16096.
-
(1997)
Biochemistry
, vol.36
, pp. 16087-16096
-
-
Feese, M.D.1
Comolli, L.2
Meadow, N.D.3
Roseman, S.4
Remington, S.J.5
-
39
-
-
0032521383
-
The structure of the Escherichia coli phosphotransferase IIAmannitol reveals a novel fold with two conformations of the active site
-
van Montfort RL, Pijning T, Kalk KH, Hangyi I, Kouwijzer ML, Robillard GT, Dijkstra BW. The structure of the Escherichia coli phosphotransferase IIAmannitol reveals a novel fold with two conformations of the active site. Structure 1998;6:377-388.
-
(1998)
Structure
, vol.6
, pp. 377-388
-
-
van Montfort, R.L.1
Pijning, T.2
Kalk, K.H.3
Hangyi, I.4
Kouwijzer, M.L.5
Robillard, G.T.6
Dijkstra, B.W.7
-
40
-
-
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
-
41
-
-
0011542799
-
The Pfam protein families database
-
Bateman A, Birney E, Cerruti L, Durbin R, Etwiller L, Eddy SR, Griffiths-Jones S, Howe KL, Marshall M, Sonnhammer EL. The Pfam protein families database. Nucleic Acids Res 2002;30:276-280.
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 276-280
-
-
Bateman, A.1
Birney, E.2
Cerruti, L.3
Durbin, R.4
Etwiller, L.5
Eddy, S.R.6
Griffiths-Jones, S.7
Howe, K.L.8
Marshall, M.9
Sonnhammer, E.L.10
-
42
-
-
0032568655
-
SMART, a simple modular architecture research tool1, identification of signaling domains
-
Schultz J, Milpetz F, Bork P, Ponting CP SMART, a simple modular architecture research tool1, identification of signaling domains. Proc Natl Acad Sci USA 1998;95:5857-5864.
-
(1998)
Proc Natl Acad Sci USA
, vol.95
, pp. 5857-5864
-
-
Schultz, J.1
Milpetz, F.2
Bork, P.3
Ponting, C.P.4
-
43
-
-
0027968068
-
CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
-
Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994;22:4673-4680.
-
(1994)
Nucleic Acids Res
, vol.22
, pp. 4673-4680
-
-
Thompson, J.D.1
Higgins, D.G.2
Gibson, T.J.3
-
45
-
-
0027180507
-
Verification of protein structures: Patterns of nonbonded atomic interactions
-
Colovos C, Yeates TO. Verification of protein structures: patterns of nonbonded atomic interactions. Protein Sci 1993;2:1511-1519.
-
(1993)
Protein Sci
, vol.2
, pp. 1511-1519
-
-
Colovos, C.1
Yeates, T.O.2
-
47
-
-
0034193510
-
Protein docking using spherical polar Fourier correlations
-
Ritchie DW, Kemp GJ. Protein docking using spherical polar Fourier correlations. Proteins 2000;39:178-194.
-
(2000)
Proteins
, vol.39
, pp. 178-194
-
-
Ritchie, D.W.1
Kemp, G.J.2
-
48
-
-
21644458085
-
Development and testing of an automated approach to protein docking
-
Tovchigrechko A, Vakser IA. Development and testing of an automated approach to protein docking. Proteins 2005;60:296-301.
-
(2005)
Proteins
, vol.60
, pp. 296-301
-
-
Tovchigrechko, A.1
Vakser, I.A.2
-
49
-
-
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
-
50
-
-
0030908273
-
Advances in comparative protein-structure modelling
-
Sanchez R, Sali A. Advances in comparative protein-structure modelling. Curr Opin Struct Biol 1997;7:206-214.
-
(1997)
Curr Opin Struct Biol
, vol.7
, pp. 206-214
-
-
Sanchez, R.1
Sali, A.2
-
51
-
-
0033873929
-
Comparative protein structure modeling of genes and genomes
-
Marti-Renom MA, Stuart AC, Fiser A, Sanchez R, Melo F, Sali A. Comparative protein structure modeling of genes and genomes. Annu Rev Biophys Biomol Struct 2000;29:291-325.
-
(2000)
Annu Rev Biophys Biomol Struct
, vol.29
, pp. 291-325
-
-
Marti-Renom, M.A.1
Stuart, A.C.2
Fiser, A.3
Sanchez, R.4
Melo, F.5
Sali, A.6
-
52
-
-
0028871814
-
Evaluation of comparative protein modeling by MODELLER
-
Sali A, Potterton L, Yuan F, van Vlijmen H, Karplus M. Evaluation of comparative protein modeling by MODELLER. Proteins 1995;23:318-326.
-
(1995)
Proteins
, vol.23
, pp. 318-326
-
-
Sali, A.1
Potterton, L.2
Yuan, F.3
van Vlijmen, H.4
Karplus, M.5
-
53
-
-
17744364070
-
Improved side-chain modeling for protein-protein docking
-
Wang C, Schueler-Furman O, Baker D. Improved side-chain modeling for protein-protein docking. Protein Sci 2005;14:1328-1339.
-
(2005)
Protein Sci
, vol.14
, pp. 1328-1339
-
-
Wang, C.1
Schueler-Furman, O.2
Baker, D.3
-
54
-
-
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
-
55
-
-
2642518000
-
Hydrophobic complementarity in protein-protein docking
-
Berchanski A, Shapira B, Eisenstein M. Hydrophobic complementarity in protein-protein docking. Proteins 2004;56:130-142.
-
(2004)
Proteins
, vol.56
, pp. 130-142
-
-
Berchanski, A.1
Shapira, B.2
Eisenstein, M.3
-
56
-
-
0037683565
-
Evaluation of protein docking predictions using Hex 3.1 in CAPRI rounds 1 and 2
-
Ritchie DW. Evaluation of protein docking predictions using Hex 3.1 in CAPRI rounds 1 and 2. Proteins 2003;52:98-106.
-
(2003)
Proteins
, vol.52
, pp. 98-106
-
-
Ritchie, D.W.1
-
57
-
-
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
-
58
-
-
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
-
59
-
-
33646148965
-
Combining NMR relaxation with chemical shift perturbation data to drive protein-protein docking
-
van Dijk AD, Kaptein R, Boelens R, Bonvin AM. Combining NMR relaxation with chemical shift perturbation data to drive protein-protein docking. J Biomol NMR 2006;34:237-244.
-
(2006)
J Biomol NMR
, vol.34
, pp. 237-244
-
-
van Dijk, A.D.1
Kaptein, R.2
Boelens, R.3
Bonvin, A.M.4
-
60
-
-
28644442113
-
Refinement of unbound protein docking studies using biological knowledge
-
Heuser P, Bau D, Benkert P, Schomburg D. Refinement of unbound protein docking studies using biological knowledge. Proteins 2005;61:1059-1067.
-
(2005)
Proteins
, vol.61
, pp. 1059-1067
-
-
Heuser, P.1
Bau, D.2
Benkert, P.3
Schomburg, D.4
-
61
-
-
15244355250
-
The relationship between the flexibility of proteins and their conformational states on forming protein-protein complexes with an application to protein-protein docking
-
Smith GR, Sternberg MJ, Bates PA. The relationship between the flexibility of proteins and their conformational states on forming protein-protein complexes with an application to protein-protein docking. J Mol Biol 2005;347:1077-1101.
-
(2005)
J Mol Biol
, vol.347
, pp. 1077-1101
-
-
Smith, G.R.1
Sternberg, M.J.2
Bates, P.A.3
-
62
-
-
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
-
63
-
-
11144254064
-
An efficient molecular docking using conformational space annealing
-
Lee K, Czaplewski C, Kim SY, Lee J. An efficient molecular docking using conformational space annealing. J Comput Chem 2005;26:78-87.
-
(2005)
J Comput Chem
, vol.26
, pp. 78-87
-
-
Lee, K.1
Czaplewski, C.2
Kim, S.Y.3
Lee, J.4
-
64
-
-
26444587477
-
Refinement of protein cores and protein-peptide interfaces using a potential scaling approach
-
Riemann RN, Zacharias M. Refinement of protein cores and protein-peptide interfaces using a potential scaling approach. Protein Eng Des Sel 2005;18:465-476.
-
(2005)
Protein Eng Des Sel
, vol.18
, pp. 465-476
-
-
Riemann, R.N.1
Zacharias, M.2
-
65
-
-
33645961330
-
Flexible protein-protein docking
-
Bonvin AM. Flexible protein-protein docking. Curr Opin Struct Biol 2006;16:194-200.
-
(2006)
Curr Opin Struct Biol
, vol.16
, pp. 194-200
-
-
Bonvin, A.M.1
-
66
-
-
33646472024
-
High-resolution protein-protein docking
-
Gray JJ. High-resolution protein-protein docking. Curr Opin Struct Biol 2006;16:183-193.
-
(2006)
Curr Opin Struct Biol
, vol.16
, pp. 183-193
-
-
Gray, J.J.1
-
67
-
-
0031582083
-
Novel knowledge-based mean force potential at atomic level
-
Melo F, Feytmans E. Novel knowledge-based mean force potential at atomic level. J Mol Biol 1997;267:207-222.
-
(1997)
J Mol Biol
, vol.267
, pp. 207-222
-
-
Melo, F.1
Feytmans, E.2
-
68
-
-
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
-
69
-
-
0042375854
-
Structure-function relationship of serine protease-protein inhibitor interaction
-
Otlewski J, Jaskolski M, Buczek O, Cierpicki T, Czapinska H, Krowarsch D, Smalas AO, Stachowiak D, Szpineta A, Dadlez M. Structure-function relationship of serine protease-protein inhibitor interaction. Acta Biochim Pol 2001;48:419-428.
-
(2001)
Acta Biochim Pol
, vol.48
, pp. 419-428
-
-
Otlewski, J.1
Jaskolski, M.2
Buczek, O.3
Cierpicki, T.4
Czapinska, H.5
Krowarsch, D.6
Smalas, A.O.7
Stachowiak, D.8
Szpineta, A.9
Dadlez, M.10
|