-
1
-
-
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
-
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
-
-
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
-
4
-
-
17344380633
-
ICM-DISCO docking by global energy optimization with fully flexible side-chains
-
Fernandez-Recio J, Totrov M, Abagyan R. ICM-DISCO docking by global energy optimization with fully flexible side-chains. Proteins 2003;52:113-117.
-
(2003)
Proteins
, vol.52
, pp. 113-117
-
-
Fernandez-Recio, J.1
Totrov, M.2
Abagyan, R.3
-
5
-
-
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
-
6
-
-
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
-
7
-
-
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
-
8
-
-
0038021436
-
Assessment of blind predictions of protein-protein interactions: Current status of docking methods
-
Mendez R, Leplae R, De Maria L, 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
-
-
Mendez, R.1
Leplae, R.2
De Maria, L.3
Wodak, S.J.4
-
9
-
-
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
-
10
-
-
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
-
11
-
-
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
-
12
-
-
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
-
13
-
-
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
-
14
-
-
34548861782
-
Protein-protein docking with backbone flexibility
-
DOI: http:///10.1016/j.jmb.2007.07.050
-
Wang C, Bradley P, Baker D. Protein-protein docking with backbone flexibility. J Mol Biol; DOI: http://dx.doi.org/10.1016/j.jmb.2007.07.050.
-
J Mol Biol
-
-
Wang, C.1
Bradley, P.2
Baker, D.3
-
15
-
-
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
-
16
-
-
27344449197
-
Progress in modeling of protein structures and interactions
-
Schueler-Furman O, Wang C, Bradley P, Misura K, Baker D. Progress in modeling of protein structures and interactions. Science 2005;310:638-642.
-
(2005)
Science
, vol.310
, pp. 638-642
-
-
Schueler-Furman, O.1
Wang, C.2
Bradley, P.3
Misura, K.4
Baker, D.5
-
17
-
-
21644459373
-
Progress in protein-protein docking: Atomic resolution predictions in the CAPRI experiment using RosettaDock with an improved treatment of side-chain flexibility
-
Schueler-Furman O, Wang C, Baker D. Progress in protein-protein docking: atomic resolution predictions in the CAPRI experiment using RosettaDock with an improved treatment of side-chain flexibility. Proteins 2005;60:187-194.
-
(2005)
Proteins
, vol.60
, pp. 187-194
-
-
Schueler-Furman, O.1
Wang, C.2
Baker, D.3
-
18
-
-
36749004258
-
Funnel hunting in a rough terrain: Learning and discriminating native energy funnels
-
Submitted
-
London N, Schueler-Furman O. Funnel hunting in a rough terrain: learning and discriminating native energy funnels. Submitted.
-
-
-
London, N.1
Schueler-Furman, O.2
-
20
-
-
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
-
21
-
-
23244436580
-
Optimal clustering for detecting near-native conformations in protein docking
-
Kozakov D, Clodfelter KH, Vajda S, Camacho CJ. Optimal clustering for detecting near-native conformations in protein docking. Biophys J 2005;89:867-875.
-
(2005)
Biophys J
, vol.89
, pp. 867-875
-
-
Kozakov, D.1
Clodfelter, K.H.2
Vajda, S.3
Camacho, C.J.4
-
22
-
-
0345564859
-
Cellulosome assembly revealed by the crystal structure of the cohesin-dockerin complex
-
Carvalho AL, Dias FM, Prates JA, Nagy T, Gilbert HJ, Davies GJ, Ferreira LM, Romao MJ, Fontes CM. Cellulosome assembly revealed by the crystal structure of the cohesin-dockerin complex. Proc Natl Acad Sci USA 2003;100:13809-13814.
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 13809-13814
-
-
Carvalho, A.L.1
Dias, F.M.2
Prates, J.A.3
Nagy, T.4
Gilbert, H.J.5
Davies, G.J.6
Ferreira, L.M.7
Romao, M.J.8
Fontes, C.M.9
-
23
-
-
27744467202
-
Crystal structure of the complex between the monomeric form of Toxoplasma gondii surface antigen 1 (SAG1) and a monoclonal antibody that mimics the human immune response
-
Graille M, Stura EA, Bossus M, Muller BH, Letourneur O, Battail-Poirot N, Sibai G, Gauthier M, Rolland D, Le Du MH, Ducancel F. Crystal structure of the complex between the monomeric form of Toxoplasma gondii surface antigen 1 (SAG1) and a monoclonal antibody that mimics the human immune response. J Mol Biol 2005;354:447-458.
-
(2005)
J Mol Biol
, vol.354
, pp. 447-458
-
-
Graille, M.1
Stura, E.A.2
Bossus, M.3
Muller, B.H.4
Letourneur, O.5
Battail-Poirot, N.6
Sibai, G.7
Gauthier, M.8
Rolland, D.9
Le Du, M.H.10
Ducancel, F.11
-
24
-
-
3042547846
-
Structural basis of protein phosphatase 1 regulation
-
Terrak M, Kerff F, Langsetmo K, Tao T, Dominguez R. Structural basis of protein phosphatase 1 regulation. Nature 2004;429:780-784.
-
(2004)
Nature
, vol.429
, pp. 780-784
-
-
Terrak, M.1
Kerff, F.2
Langsetmo, K.3
Tao, T.4
Dominguez, R.5
-
25
-
-
2342447390
-
Structural inhibition of the colicin D tRNase by the tRNA-mimicking immunity protein
-
Graille M, Mora L, Buckingham RH, van Tilbeurgh H, de Zamaroczy M. Structural inhibition of the colicin D tRNase by the tRNA-mimicking immunity protein. EMBO J 2004;23:1474-1482.
-
(2004)
EMBO J
, vol.23
, pp. 1474-1482
-
-
Graille, M.1
Mora, L.2
Buckingham, R.H.3
van Tilbeurgh, H.4
de Zamaroczy, M.5
-
26
-
-
4143057133
-
Structural basis for inhibition of Aspergillus niger xylanase by triticum aestivum xylanase inhibitor-I
-
Sansen S, De Ranter CJ, Gebruers K, Brijs K, Courtin CM, Delcour JA, Rabijns A. Structural basis for inhibition of Aspergillus niger xylanase by triticum aestivum xylanase inhibitor-I. J Biol Chem 2004;279:36022-36028.
-
(2004)
J Biol Chem
, vol.279
, pp. 36022-36028
-
-
Sansen, S.1
De Ranter, C.J.2
Gebruers, K.3
Brijs, K.4
Courtin, C.M.5
Delcour, J.A.6
Rabijns, A.7
-
27
-
-
3142683624
-
Insight into the PrPC→PrPSc conversion from the structures of antibody-bound ovine prion scrapie-susceptibility variants
-
Eghiaian F, Grosclaude J, Lesceu S, Debey P, Doublet B, Treguer E, Rezaei H, Knossow M. Insight into the PrPC→PrPSc conversion from the structures of antibody-bound ovine prion scrapie-susceptibility variants. Proc Natl Acad Sci USA 2004;101:10254-10259.
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, pp. 10254-10259
-
-
Eghiaian, F.1
Grosclaude, J.2
Lesceu, S.3
Debey, P.4
Doublet, B.5
Treguer, E.6
Rezaei, H.7
Knossow, M.8
-
28
-
-
20844445832
-
Structural basis of the Sir1-origin recognition complex interaction in transcriptional silencing
-
Hou Z, Bernstein DA, Fox CA, Keck JL. Structural basis of the Sir1-origin recognition complex interaction in transcriptional silencing. Proc Natl Acad Sci USA 2005;102:8489-8494.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 8489-8494
-
-
Hou, Z.1
Bernstein, D.A.2
Fox, C.A.3
Keck, J.L.4
-
29
-
-
34247244814
-
Structural basis for ARF1-mediated recruitment of ARHGAP21 to Golgi membranes
-
Menetrey J, Perderiset M, Cicolari J, Dubois T, Elkhatib N, El Khadali F, Franco M, Chavrier P, Houdusse A. Structural basis for ARF1-mediated recruitment of ARHGAP21 to Golgi membranes. EMBO J 2007;26:1953-1962.
-
(2007)
EMBO J
, vol.26
, pp. 1953-1962
-
-
Menetrey, J.1
Perderiset, M.2
Cicolari, J.3
Dubois, T.4
Elkhatib, N.5
El Khadali, F.6
Franco, M.7
Chavrier, P.8
Houdusse, A.9
-
30
-
-
34247473840
-
Molecular mimicry enables competitive recruitment by a natively disordered protein
-
Bonsor DA, Grishkovskaya I, Dodson EJ, Kleanthous C. Molecular mimicry enables competitive recruitment by a natively disordered protein. J Am Chem Soc 2007;129:4800-4807.
-
(2007)
J Am Chem Soc
, vol.129
, pp. 4800-4807
-
-
Bonsor, D.A.1
Grishkovskaya, I.2
Dodson, E.J.3
Kleanthous, C.4
-
31
-
-
34548726434
-
A novel and unexpected complex between the SUMO-1-conjugating enzyme UBC9 and the ubiquitin-conjugating enzyme E2-25 kDa
-
in press
-
Walker JR, Awakumov GV, Xue S, Newman EM, Mackenzie F, Weigelt J, Sundstrom M, Arrowsmith CH, Edwards AM, Bochkarev A, Dhe-Paganon S. A novel and unexpected complex between the SUMO-1-conjugating enzyme UBC9 and the ubiquitin-conjugating enzyme E2-25 kDa, in press.
-
-
-
Walker, J.R.1
Awakumov, G.V.2
Xue, S.3
Newman, E.M.4
Mackenzie, F.5
Weigelt, J.6
Sundstrom, M.7
Arrowsmith, C.H.8
Edwards, A.M.9
Bochkarev, A.10
Dhe-Paganon, S.11
-
33
-
-
4444221565
-
UCSF Chimera - a visualization system for exploratory research and analysis
-
Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE. UCSF Chimera - a visualization system for exploratory research and analysis. J Comput Chem 2004;25:1605-1612.
-
(2004)
J Comput Chem
, vol.25
, pp. 1605-1612
-
-
Pettersen, E.F.1
Goddard, T.D.2
Huang, C.C.3
Couch, G.S.4
Greenblatt, D.M.5
Meng, E.C.6
Ferrin, T.E.7
-
34
-
-
12944257228
-
The ConSurf-HSSP database: The mapping of evolutionary conservation among homologs onto PDB structures
-
Glaser F, Rosenberg Y, Kessel A, Pupko T, Ben-Tal N. The ConSurf-HSSP database: the mapping of evolutionary conservation among homologs onto PDB structures. Proteins 2005;58:610-617.
-
(2005)
Proteins
, vol.58
, pp. 610-617
-
-
Glaser, F.1
Rosenberg, Y.2
Kessel, A.3
Pupko, T.4
Ben-Tal, N.5
-
36
-
-
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
-
38
-
-
0002714543
-
Making large-scale SVM learning practical
-
Schoelkopf C, Burges C, Smola A, editors, Cambridge, MA: MIT Press;
-
Joachims T. Making large-scale SVM learning practical. In: Schoelkopf C, Burges C, Smola A, editors. Advances in kernel methods - support vector learning. Cambridge, MA: MIT Press; 1999. pp 41-56.
-
(1999)
Advances in kernel methods - support vector learning
, pp. 41-56
-
-
Joachims, T.1
-
39
-
-
0036161259
-
Gene selection for cancer classification using support vector machines
-
Guyon I, Weston J, Barnhill S, Vapnik V. Gene selection for cancer classification using support vector machines. Machine Learning 2002;46:389-422.
-
(2002)
Machine Learning
, vol.46
, pp. 389-422
-
-
Guyon, I.1
Weston, J.2
Barnhill, S.3
Vapnik, V.4
-
40
-
-
0034822446
-
Anti-SAG1 peptide antibodies inhibit the penetration of Toxoplasma gondii tachyzoites into enterocyte cell lines
-
Velge-Roussel F, Dimier-Poisson I, Buzoni-Gatel D, Bout D. Anti-SAG1 peptide antibodies inhibit the penetration of Toxoplasma gondii tachyzoites into enterocyte cell lines. Parasitology 2001;123:225-233.
-
(2001)
Parasitology
, vol.123
, pp. 225-233
-
-
Velge-Roussel, F.1
Dimier-Poisson, I.2
Buzoni-Gatel, D.3
Bout, D.4
-
41
-
-
0345832301
-
ClusPro: An automated docking and discrimination method for the prediction of protein complexes
-
Comeau SR, Gatchell DW, Vajda S, Camacho CJ. ClusPro: an automated docking and discrimination method for the prediction of protein complexes. Bioinformatics 2004;20:45-50.
-
(2004)
Bioinformatics
, vol.20
, pp. 45-50
-
-
Comeau, S.R.1
Gatchell, D.W.2
Vajda, S.3
Camacho, C.J.4
-
42
-
-
34248513078
-
ZRANK: Reranking protein docking predictions with an optimized energy function
-
Pierce B, Weng Z. ZRANK: reranking protein docking predictions with an optimized energy function. Proteins 2007;67:1078-1086.
-
(2007)
Proteins
, vol.67
, pp. 1078-1086
-
-
Pierce, B.1
Weng, Z.2
-
43
-
-
21644447570
-
Improving CAPRI predictions: Optimized desolvation for rigid-body docking
-
Fernandez-Recio J, Abagyan R, Totrov M. Improving CAPRI predictions: optimized desolvation for rigid-body docking. Proteins 2005;60:308-313.
-
(2005)
Proteins
, vol.60
, pp. 308-313
-
-
Fernandez-Recio, J.1
Abagyan, R.2
Totrov, M.3
-
44
-
-
33646044395
-
WHISCY: What information does surface conservation yield? Application to data-driven docking
-
de Vries SJ, van Dijk AD, Bonvin AM. WHISCY: what information does surface conservation yield? Application to data-driven docking. Proteins 2006;63:479-489.
-
(2006)
Proteins
, vol.63
, pp. 479-489
-
-
de Vries, S.J.1
van Dijk, A.D.2
Bonvin, A.M.3
-
45
-
-
34047129815
-
A new protein-protein docking scoring function based on interface residue properties
-
Bernauer J, Aze J, Janin J, Poupon A. A new protein-protein docking scoring function based on interface residue properties. Bioinformatics 2007;23:555-562.
-
(2007)
Bioinformatics
, vol.23
, pp. 555-562
-
-
Bernauer, J.1
Aze, J.2
Janin, J.3
Poupon, A.4
-
46
-
-
0038359612
-
Finding needles in haystacks: Reranking DOT results by using shape complementarity, cluster analysis, and biological information
-
Law DS, Ten Eyck LF, Katzenelson O, Tsigelny I, Roberts VA, Pique ME, Mitchell JC. Finding needles in haystacks: reranking DOT results by using shape complementarity, cluster analysis, and biological information. Proteins 2003;52:33-40.
-
(2003)
Proteins
, vol.52
, pp. 33-40
-
-
Law, D.S.1
Ten Eyck, L.F.2
Katzenelson, O.3
Tsigelny, I.4
Roberts, V.A.5
Pique, M.E.6
Mitchell, J.C.7
|