-
1
-
-
77957948556
-
Blind predictions of protein interfaces by docking calculations in CAPRI
-
Lensink MF, Wodak SJ, (2010) Blind predictions of protein interfaces by docking calculations in CAPRI. Proteins 78: 3085-3095.
-
(2010)
Proteins
, vol.78
, pp. 3085-3095
-
-
Lensink, M.F.1
Wodak, S.J.2
-
2
-
-
77957934896
-
Docking and scoring protein interactions: CAPRI 2009
-
Lensink MF, Wodak SJ, (2010) Docking and scoring protein interactions: CAPRI 2009. Proteins 78: 3073-3084.
-
(2010)
Proteins
, vol.78
, pp. 3073-3084
-
-
Lensink, M.F.1
Wodak, S.J.2
-
3
-
-
36749098356
-
The performance of ZDOCK and ZRANK in rounds 6-11 of CAPRI
-
Wiehe K, Pierce B, Tong WW, Hwang H, Mintseris J, et al. (2007) The performance of ZDOCK and ZRANK in rounds 6-11 of CAPRI. Proteins 69: 719-725.
-
(2007)
Proteins
, vol.69
, pp. 719-725
-
-
Wiehe, K.1
Pierce, B.2
Tong, W.W.3
Hwang, H.4
Mintseris, J.5
-
4
-
-
0345832301
-
ClusPro: an automated docking and discrimination method for the prediction of protein complexes
-
Comeau SR, Gatchell DW, Vajda S, Camacho CJ, (2004) ClusPro: an automated docking and discrimination method for the prediction of protein complexes. Bioinformatics 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
-
5
-
-
0037442962
-
HADDOCK: a protein-protein docking approach based on biochemical or biophysical information
-
Dominguez C, Boelens R, Bonvin AM, (2003) HADDOCK: a protein-protein docking approach based on biochemical or biophysical information. J Am Chem Soc 125: 1731-1737.
-
(2003)
J Am Chem Soc
, vol.125
, pp. 1731-1737
-
-
Dominguez, C.1
Boelens, R.2
Bonvin, A.M.3
-
6
-
-
34548861782
-
Protein-protein docking with backbone flexibility
-
Wang C, Bradley P, Baker D, (2007) Protein-protein docking with backbone flexibility. J Mol Biol 373: 503-519.
-
(2007)
J Mol Biol
, vol.373
, pp. 503-519
-
-
Wang, C.1
Bradley, P.2
Baker, D.3
-
7
-
-
36749075510
-
Incorporating biochemical information and backbone flexibility in RosettaDock for CAPRI rounds 6-12
-
Chaudhury S, Sircar A, Sivasubramanian A, Berrondo M, Gray JJ, (2007) Incorporating biochemical information and backbone flexibility in RosettaDock for CAPRI rounds 6-12. Proteins 69: 793-800.
-
(2007)
Proteins
, vol.69
, pp. 793-800
-
-
Chaudhury, S.1
Sircar, A.2
Sivasubramanian, A.3
Berrondo, M.4
Gray, J.J.5
-
8
-
-
77957966065
-
A generalized approach to sampling backbone conformations with RosettaDock for CAPRI rounds 13-19
-
Sircar A, Chaudhury S, Kilambi KP, Berrondo M, Gray JJ, (2010) A generalized approach to sampling backbone conformations with RosettaDock for CAPRI rounds 13-19. Proteins 78: 3115-3123.
-
(2010)
Proteins
, vol.78
, pp. 3115-3123
-
-
Sircar, A.1
Chaudhury, S.2
Kilambi, K.P.3
Berrondo, M.4
Gray, J.J.5
-
9
-
-
77957943551
-
Rosetta in CAPRI rounds 13-19
-
Fleishman SJ, Corn JE, Strauch EM, Whitehead TA, Andre I, et al. (2010) Rosetta in CAPRI rounds 13-19. Proteins 78: 3212-3218.
-
(2010)
Proteins
, vol.78
, pp. 3212-3218
-
-
Fleishman, S.J.1
Corn, J.E.2
Strauch, E.M.3
Whitehead, T.A.4
Andre, I.5
-
10
-
-
44949117092
-
A combination of rescoring and refinement significantly improves protein docking performance
-
Pierce B, Weng Z, (2008) A combination of rescoring and refinement significantly improves protein docking performance. Proteins 72: 270-279.
-
(2008)
Proteins
, vol.72
, pp. 270-279
-
-
Pierce, B.1
Weng, Z.2
-
11
-
-
33644839662
-
Structural model of the mAb 806-EGFR complex using computational docking followed by computational and experimental mutagenesis
-
Sivasubramanian A, Chao G, Pressler HM, Wittrup KD, Gray JJ, (2006) Structural model of the mAb 806-EGFR complex using computational docking followed by computational and experimental mutagenesis. Structure 14: 401-414.
-
(2006)
Structure
, vol.14
, pp. 401-414
-
-
Sivasubramanian, A.1
Chao, G.2
Pressler, H.M.3
Wittrup, K.D.4
Gray, J.J.5
-
12
-
-
37349109629
-
Modeling the structure of mAb 14B7 bound to the anthrax protective antigen
-
Sivasubramanian A, Maynard JA, Gray JJ, (2008) Modeling the structure of mAb 14B7 bound to the anthrax protective antigen. Proteins 70: 218-230.
-
(2008)
Proteins
, vol.70
, pp. 218-230
-
-
Sivasubramanian, A.1
Maynard, J.A.2
Gray, J.J.3
-
13
-
-
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, et al. (2003) Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. J Mol Biol 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
-
14
-
-
48449094112
-
Conformer selection and induced fit in flexible backbone protein-protein docking using computational and NMR ensembles
-
Chaudhury S, Gray JJ, (2008) Conformer selection and induced fit in flexible backbone protein-protein docking using computational and NMR ensembles. J Mol Biol 381: 1068-1087.
-
(2008)
J Mol Biol
, vol.381
, pp. 1068-1087
-
-
Chaudhury, S.1
Gray, J.J.2
-
15
-
-
76749153896
-
SnugDock: paratope structural optimization during antibody-antigen docking compensates for errors in antibody homology models
-
Sircar A, Gray JJ, (2010) SnugDock: paratope structural optimization during antibody-antigen docking compensates for errors in antibody homology models. PLoS Comput Biol 6: e1000644.
-
(2010)
PLoS Comput Biol
, vol.6
-
-
Sircar, A.1
Gray, J.J.2
-
16
-
-
71049127018
-
Identification of structural mechanisms of HIV-1 protease specificity using computational peptide docking: implications for drug resistance
-
Chaudhury S, Gray JJ, (2009) Identification of structural mechanisms of HIV-1 protease specificity using computational peptide docking: implications for drug resistance. Structure 17: 1636-1648.
-
(2009)
Structure
, vol.17
, pp. 1636-1648
-
-
Chaudhury, S.1
Gray, J.J.2
-
17
-
-
77953573815
-
Sub-angstrom modeling of complexes between flexible peptides and globular proteins
-
Raveh B, London N, Schueler-Furman O, (2010) Sub-angstrom modeling of complexes between flexible peptides and globular proteins. Proteins 78: 2029-2040.
-
(2010)
Proteins
, vol.78
, pp. 2029-2040
-
-
Raveh, B.1
London, N.2
Schueler-Furman, O.3
-
18
-
-
79952789526
-
Mechanism of polyubiquitin chain recognition by the human ubiquitin conjugating enzyme Ube2g2
-
Bocik WE, Sircar A, Gray JJ, Tolman JR, (2011) Mechanism of polyubiquitin chain recognition by the human ubiquitin conjugating enzyme Ube2g2. J Biol Chem 286: 3981-3991.
-
(2011)
J Biol Chem
, vol.286
, pp. 3981-3991
-
-
Bocik, W.E.1
Sircar, A.2
Gray, J.J.3
Tolman, J.R.4
-
19
-
-
55849144771
-
Emergence of symmetry in homooligomeric biological assemblies
-
Andre I, Strauss CE, Kaplan DB, Bradley P, Baker D, (2008) Emergence of symmetry in homooligomeric biological assemblies. Proc Natl Acad Sci U S A 105: 16148-16152.
-
(2008)
Proc Natl Acad Sci U S A
, vol.105
, pp. 16148-16152
-
-
Andre, I.1
Strauss, C.E.2
Kaplan, D.B.3
Bradley, P.4
Baker, D.5
-
20
-
-
0031585984
-
Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions
-
Simons KT, Kooperberg C, Huang E, Baker D, (1997) Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. J Mol Biol 268: 209-225.
-
(1997)
J Mol Biol
, vol.268
, pp. 209-225
-
-
Simons, K.T.1
Kooperberg, C.2
Huang, E.3
Baker, D.4
-
21
-
-
78650905964
-
ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules
-
Leaver-Fay A, Tyka M, Lewis SM, Lange OF, Thompson J, et al. (2011) ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules. Methods Enzymol 487: 545-574.
-
(2011)
Methods Enzymol
, vol.487
, pp. 545-574
-
-
Leaver-Fay, A.1
Tyka, M.2
Lewis, S.M.3
Lange, O.F.4
Thompson, J.5
-
22
-
-
79960997212
-
RosettaScripts: an XML interface to the Rosetta suite of macromolecular modeling
-
Fleishman SJ, Corn JE, (2011) RosettaScripts: an XML interface to the Rosetta suite of macromolecular modeling. PLoS One.
-
(2011)
PLoS One
-
-
Fleishman, S.J.1
Corn, J.E.2
-
23
-
-
77949617607
-
PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta
-
Chaudhury S, Lyskov S, Gray JJ, (2010) PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta. Bioinformatics 26: 689-691.
-
(2010)
Bioinformatics
, vol.26
, pp. 689-691
-
-
Chaudhury, S.1
Lyskov, S.2
Gray, J.J.3
-
25
-
-
58149094776
-
RosettaLigand docking with full ligand and receptor flexibility
-
Davis IW, Baker D, (2009) RosettaLigand docking with full ligand and receptor flexibility. J Mol Biol 385: 381-392.
-
(2009)
J Mol Biol
, vol.385
, pp. 381-392
-
-
Davis, I.W.1
Baker, D.2
-
26
-
-
57349132441
-
Protein-protein docking benchmark version 3.0
-
Hwang H, Pierce B, Mintseris J, Janin J, Weng Z, (2008) Protein-protein docking benchmark version 3.0. Proteins 73: 705-709.
-
(2008)
Proteins
, vol.73
, pp. 705-709
-
-
Hwang, H.1
Pierce, B.2
Mintseris, J.3
Janin, J.4
Weng, Z.5
-
27
-
-
17744364070
-
Improved side-chain modeling for protein-protein docking
-
Wang C, Schueler-Furman O, Baker D, (2005) Improved side-chain modeling for protein-protein docking. Protein Sci 14: 1328-1339.
-
(2005)
Protein Sci
, vol.14
, pp. 1328-1339
-
-
Wang, C.1
Schueler-Furman, O.2
Baker, D.3
-
28
-
-
21644489506
-
CAPRI rounds 3-5 reveal promising successes and future challenges for RosettaDock
-
Daily MD, Masica D, Sivasubramanian A, Somarouthu S, Gray JJ, (2005) CAPRI rounds 3-5 reveal promising successes and future challenges for RosettaDock. Proteins 60: 181-186.
-
(2005)
Proteins
, vol.60
, pp. 181-186
-
-
Daily, M.D.1
Masica, D.2
Sivasubramanian, A.3
Somarouthu, S.4
Gray, J.J.5
-
29
-
-
0033954256
-
The Protein Data Bank
-
Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, et al. (2000) The Protein Data Bank. Nucleic Acids Res 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
-
30
-
-
21644480883
-
Protein-Protein Docking Benchmark 2.0: an update
-
Mintseris J, Wiehe K, Pierce B, Anderson R, Chen R, et al. (2005) Protein-Protein Docking Benchmark 2.0: an update. Proteins 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
-
31
-
-
0038021436
-
Assessment of blind predictions of protein-protein interactions: Current status of docking methods
-
Méndez R, Leplae R, De Maria L, Wodak SJ, (2003) Assessment of blind predictions of protein-protein interactions: Current status of docking methods. Proteins: Structure, Function, and Genetics 52: 51-67.
-
(2003)
Proteins: Structure, Function, and Genetics
, vol.52
, pp. 51-67
-
-
Méndez, R.1
Leplae, R.2
de Maria, L.3
Wodak, S.J.4
-
32
-
-
0038021436
-
Assessment of blind predictions of protein-protein interactions: current status of docking methods
-
Mendez R, Leplae R, De Maria L, Wodak SJ, (2003) Assessment of blind predictions of protein-protein interactions: current status of docking methods. Proteins 52: 51-67.
-
(2003)
Proteins
, vol.52
, pp. 51-67
-
-
Mendez, R.1
Leplae, R.2
de Maria, L.3
Wodak, S.J.4
-
33
-
-
0002344794
-
Bootstrap methods: another look at the jackknife Annals of Statistics
-
Efron B, (1979) Bootstrap methods: another look at the jackknife Annals of Statistics 7: 1-26.
-
(1979)
, vol.7
, pp. 1-26
-
-
Efron, B.1
-
34
-
-
0036305947
-
Mechanism of coenzyme recognition and binding revealed by crystal structure analysis of ferredoxin-NADP+ reductase complexed with NADP+
-
Hermoso JA, Mayoral T, Faro M, Gomez-Moreno C, Sanz-Aparicio J, et al. (2002) Mechanism of coenzyme recognition and binding revealed by crystal structure analysis of ferredoxin-NADP+ reductase complexed with NADP+. J Mol Biol 319: 1133-1142.
-
(2002)
J Mol Biol
, vol.319
, pp. 1133-1142
-
-
Hermoso, J.A.1
Mayoral, T.2
Faro, M.3
Gomez-Moreno, C.4
Sanz-Aparicio, J.5
-
35
-
-
0033731168
-
Crystallographic studies of the interaction between the ferredoxin-NADP+ reductase and ferredoxin from the cyanobacterium Anabaena: looking for the elusive ferredoxin molecule
-
Morales R, Kachalova G, Vellieux F, Charon MH, Frey M, (2000) Crystallographic studies of the interaction between the ferredoxin-NADP+ reductase and ferredoxin from the cyanobacterium Anabaena: looking for the elusive ferredoxin molecule. Acta Crystallogr D Biol Crystallogr 56: 1408-1412.
-
(2000)
Acta Crystallogr D Biol Crystallogr
, vol.56
, pp. 1408-1412
-
-
Morales, R.1
Kachalova, G.2
Vellieux, F.3
Charon, M.H.4
Frey, M.5
-
36
-
-
77951650117
-
Computational predictions of the mutant behavior of AraC
-
Berrondo M, Gray JJ, Schleif R, (2010) Computational predictions of the mutant behavior of AraC. J Mol Biol 398: 462-470.
-
(2010)
J Mol Biol
, vol.398
, pp. 462-470
-
-
Berrondo, M.1
Gray, J.J.2
Schleif, R.3
|