-
1
-
-
21644440105
-
Protein-protein docking using 3D-Dock in rounds 3, 4, and 5 of CAPRI
-
Carter, P.; Lesk, V.I.; Islam, S.A.; Sternberg, M.J.E. Protein-protein docking using 3D-Dock in rounds 3, 4, and 5 of CAPRI. Proteins: Struct. Funct. Bioinf. 2005, 60, 281-288.
-
(2005)
Proteins: Struct. Funct. Bioinf
, vol.60
, pp. 281-288
-
-
Carter, P.1
Lesk, V.I.2
Islam, S.A.3
Sternberg, M.J.E.4
-
2
-
-
77149153105
-
Structural basis for the specific interaction of chicken haemoglobin with bromophenol blue: A computational analysis
-
Yu, H.; Wang, Z.L.; Qin, W.B.; Zhang, L.R. Structural basis for the specific interaction of chicken haemoglobin with bromophenol blue: A computational analysis. Mol. Phys. 2010, 108, 215-220.
-
(2010)
Mol. Phys
, vol.108
, pp. 215-220
-
-
Yu, H.1
Wang, Z.L.2
Qin, W.B.3
Zhang, L.R.4
-
3
-
-
77949382951
-
Present and future challenges and limitations in protein-protein docking
-
Pons, C.; Grosdidier, S.; Solernou, A.; Perez-Cano, L.; Fernandez-Recio, J. Present and future challenges and limitations in protein-protein docking. Proteins: Struct. Funct. Bioinf. 2010, 78, 95-108.
-
(2010)
Proteins: Struct. Funct. Bioinf
, vol.78
, pp. 95-108
-
-
Pons, C.1
Grosdidier, S.2
Solernou, A.3
Perez-Cano, L.4
Fernandez-Recio, J.5
-
4
-
-
67649124670
-
Docking and scoring: Applications to drug discovery in the interactomics era
-
Grosdidier, S.; Fernandez-Recio, J. Docking and scoring: Applications to drug discovery in the interactomics era. Expert Opin. Drug Discov. 2009, 4, 673-686.
-
(2009)
Expert Opin. Drug Discov
, vol.4
, pp. 673-686
-
-
Grosdidier, S.1
Fernandez-Recio, J.2
-
5
-
-
36749053938
-
Prediction and scoring of docking poses with pyDock
-
Grosdidier, S.; Pons, C.; Solernou, A.; Fernandez-Recio, J. Prediction and scoring of docking poses with pyDock. Proteins: Struct. Funct. Bioinf. 2007, 69, 852-858.
-
(2007)
Proteins: Struct. Funct. Bioinf
, vol.69
, pp. 852-858
-
-
Grosdidier, S.1
Pons, C.2
Solernou, A.3
Fernandez-Recio, J.4
-
6
-
-
70349882144
-
FRODOCK: A new approach for fast rotational protein-protein docking
-
Garzon, J.I.; Lopez-Blanco, J.R.; Pons, C.; Kovacs, J.; Abagyan, R.; Fernandez-Recio, J.; Chacon, P. FRODOCK: A new approach for fast rotational protein-protein docking. Bioinformatics 2009, 25, 2544-2551.
-
(2009)
Bioinformatics
, vol.25
, pp. 2544-2551
-
-
Garzon, J.I.1
Lopez-Blanco, J.R.2
Pons, C.3
Kovacs, J.4
Abagyan, R.5
Fernandez-Recio, J.6
Chacon, P.7
-
7
-
-
0034645763
-
Knowledge-based scoring function to predict protein-ligand interactions1
-
Gohlke, H.; Hendlich, M.; Klebe, G. Knowledge-based scoring function to predict protein-ligand interactions1. J. Mol. Biol. 2000, 295, 337-356.
-
(2000)
J. Mol. Biol
, vol.295
, pp. 337-356
-
-
Gohlke, H.1
Hendlich, M.2
Klebe, G.3
-
8
-
-
77957950490
-
Optimization of pyDock for the new CAPRI challenges: Docking of homology-based models, domain-domain assembly and protein-RNA binding
-
Pons, C.; Solernou, A.; Perez-Cano, L.; Grosdidier, S.; Fernandez-Recio, J. Optimization of pyDock for the new CAPRI challenges: Docking of homology-based models, domain-domain assembly and protein-RNA binding. Proteins: Struct. Funct. Bioinf. 2010, 78, 3182-3188.
-
(2010)
Proteins: Struct. Funct. Bioinf
, vol.78
, pp. 3182-3188
-
-
Pons, C.1
Solernou, A.2
Perez-Cano, L.3
Grosdidier, S.4
Fernandez-Recio, J.5
-
9
-
-
0031565730
-
Modelling protein docking using shape complementarity, electrostatics and biochemical information1
-
Gabb, H.A.; Jackson, R.M.; Sternberg, M.J.E. Modelling protein docking using shape complementarity, electrostatics and biochemical information1. 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.E.3
-
10
-
-
79956150167
-
pyDockCG: New coarse-grained potential for protein protein docking
-
Solernou, A.; Fernandez-Recio, J. pyDockCG: New coarse-grained potential for protein protein docking. J. Phys. Chem. B 2011, 115, 6032-6039.
-
(2011)
J. Phys. Chem. B
, vol.115
, pp. 6032-6039
-
-
Solernou, A.1
Fernandez-Recio, J.2
-
11
-
-
79952132540
-
Scoring by intermolecular pairwise propensities of exposed residues (SIPPER): A new efficient potential for protein-protein docking
-
Pons, C.; Talavera, D.; de la Cruz, X.; Orozco, M.; Fernandez-Recio, J. Scoring by intermolecular pairwise propensities of exposed residues (SIPPER): A new efficient potential for protein-protein docking. J. Chem. Inf. Model. 2011, 51, 370-377.
-
(2011)
J. Chem. Inf. Model
, vol.51
, pp. 370-377
-
-
Pons, C.1
Talavera, D.2
de la Cruz, X.3
Orozco, M.4
Fernandez-Recio, J.5
-
12
-
-
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: Struct. Funct. Bioinf. 2007, 67, 1078-1086.
-
(2007)
Proteins: Struct. Funct. Bioinf
, vol.67
, pp. 1078-1086
-
-
Pierce, B.1
Weng, Z.2
-
13
-
-
41449100252
-
Amino acid network and its scoring application in protein-protein docking
-
Chang, S.; Jiao, X.; Li, C.H.; Gong, X.Q.; Chen, W.Z.; Wang, C.X. Amino acid network and its scoring application in protein-protein docking. Biophys. Chem. 2008, 134, 111-118.
-
(2008)
Biophys. Chem
, vol.134
, pp. 111-118
-
-
Chang, S.1
Jiao, X.2
Li, C.H.3
Gong, X.Q.4
Chen, W.Z.5
Wang, C.X.6
-
14
-
-
77957965651
-
Protein-protein docking with binding site patch prediction and network-based terms enhanced combinatorial scoring
-
Gong, X.Q.; Wang, P.W.; Yang, F.; Chang, S.; Liu, B.; He, H.Q.; Cao, L.B.; Xu, X.J.; Li, C.H.; Chen, W.Z. et al. Protein-protein docking with binding site patch prediction and network-based terms enhanced combinatorial scoring. Proteins: Struct. Funct. Bioinf. 2010, 78, 3150-3155.
-
(2010)
Proteins: Struct. Funct. Bioinf
, vol.78
, pp. 3150-3155
-
-
Gong, X.Q.1
Wang, P.W.2
Yang, F.3
Chang, S.4
Liu, B.5
He, H.Q.6
Cao, L.B.7
Xu, X.J.8
Li, C.H.9
Chen, W.Z.10
-
15
-
-
77953931506
-
Protein docking by Rotation-Based Uniform Sampling (RotBUS) with fast computing of intermolecular contact distance and residue desolvation
-
Solernou, A.; Fernandez-Recio, J. Protein docking by Rotation-Based Uniform Sampling (RotBUS) with fast computing of intermolecular contact distance and residue desolvation. BMC Bioinf. 2010, 11, 352:1-352:14.
-
(2010)
BMC Bioinf
, vol.11
, Issue.352
-
-
Solernou, A.1
Fernandez-Recio, J.2
-
16
-
-
68249144507
-
How patchy can one get and still condense? The role of dissimilar patches in the interactions of colloidal particles
-
Tavares, J.M.; Teixeira, P.I.C.; da Gama, M.M.T. How patchy can one get and still condense? The role of dissimilar patches in the interactions of colloidal particles. Mol. Phys. 2009, 107, 453-466.
-
(2009)
Mol. Phys
, vol.107
, pp. 453-466
-
-
Tavares, J.M.1
Teixeira, P.I.C.2
da Gama, M.M.T.3
-
17
-
-
53349117774
-
High-quality binary protein interaction map of the yeast interactome network
-
Yu, H.Y.; Braun, P.; Yildirim, M.A.; Lemmens, I.; Venkatesan, K.; Sahalie, J.; Hirozane-Kishikawa, T.; Gebreab, F.; Li, N.; Simonis, N. et al. High-quality binary protein interaction map of the yeast interactome network. Science 2008, 322, 104-110.
-
(2008)
Science
, vol.322
, pp. 104-110
-
-
Yu, H.Y.1
Braun, P.2
Yildirim, M.A.3
Lemmens, I.4
Venkatesan, K.5
Sahalie, J.6
Hirozane-Kishikawa, T.7
Gebreab, F.8
Li, N.9
Simonis, N.10
-
18
-
-
52949102889
-
Crystal structure of opsin in its G-protein-interacting conformation
-
Scheerer, P.; Park, J.H.; Hildebrand, P.W.; Kim, Y.J.; Krauss, N.; Choe, H.W.; Hofmann, K.P.; Ernst, O.P. Crystal structure of opsin in its G-protein-interacting conformation. Nature 2008, 455, 497-502.
-
(2008)
Nature
, vol.455
, pp. 497-502
-
-
Scheerer, P.1
Park, J.H.2
Hildebrand, P.W.3
Kim, Y.J.4
Krauss, N.5
Choe, H.W.6
Hofmann, K.P.7
Ernst, O.P.8
-
19
-
-
41349118690
-
Small-world view of the amino acids that play a key role in protein folding
-
Vendruscolo, M.; Dokholyan, N.V.; Paci, E.; Karplus, M. Small-world view of the amino acids that play a key role in protein folding. Phys. Rev. E 2002, 65, 061910:1-061910:4.
-
(2002)
Phys. Rev. E
, vol.65
-
-
Vendruscolo, M.1
Dokholyan, N.V.2
Paci, E.3
Karplus, M.4
-
20
-
-
3042728343
-
Understanding and predicting structure-property relations in polymeric materials through molecular simulations
-
Theodorou, D.N. Understanding and predicting structure-property relations in polymeric materials through molecular simulations. Mol. Phys. 2004, 102, 147-166.
-
(2004)
Mol. Phys
, vol.102
, pp. 147-166
-
-
Theodorou, D.N.1
-
21
-
-
8544221118
-
Network analysis of protein structures identifies functional residues
-
Amitai, G.; Shemesh, A.; Sitbon, E.; Shklar, M.; Netanely, D.; Venger, I.; Pietrokovski, S. Network analysis of protein structures identifies functional residues. J. Mol. Biol. 2004, 344, 1135-1146.
-
(2004)
J. Mol. Biol
, vol.344
, pp. 1135-1146
-
-
Amitai, G.1
Shemesh, A.2
Sitbon, E.3
Shklar, M.4
Netanely, D.5
Venger, I.6
Pietrokovski, S.7
-
22
-
-
80053341922
-
Prediction of protein-binding areas by small-world residue networks and application to docking
-
Pons, C.; Glaser, F.; Fernandez-Recio, J. Prediction of protein-binding areas by small-world residue networks and application to docking. BMC Bioinf. 2011, 12, 378:1-378:10.
-
(2011)
BMC Bioinf
, vol.12
-
-
Pons, C.1
Glaser, F.2
Fernandez-Recio, J.3
-
23
-
-
77952990834
-
Network analysis of protein-protein interaction
-
Chang, S.; Gong, X.Q.; Jiao, X.; Li, C.H.; Chen, W.Z.; Wang, C.X. Network analysis of protein-protein interaction. Chin. Sci. Bull. 2010, 55, 814-822.
-
(2010)
Chin. Sci. Bull
, vol.55
, pp. 814-822
-
-
Chang, S.1
Gong, X.Q.2
Jiao, X.3
Li, C.H.4
Chen, W.Z.5
Wang, C.X.6
-
24
-
-
0037173002
-
Topological determinants of protein folding
-
Dokholyan, N.V.; Li, L.; Ding, F.; Shakhnovich, E.I. Topological determinants of protein folding. Proc. Natl. Acad. Sci. USA 2002, 99, 8637-8641.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 8637-8641
-
-
Dokholyan, N.V.1
Li, L.2
Ding, F.3
Shakhnovich, E.I.4
-
25
-
-
0346057951
-
Small-world communication of residues and significance for protein dynamics
-
Atilgan, A.R.; Akan, P.; Baysal, C. Small-world communication of residues and significance for protein dynamics. Biophys. J. 2004, 86, 85-91.
-
(2004)
Biophys. J
, vol.86
, pp. 85-91
-
-
Atilgan, A.R.1
Akan, P.2
Baysal, C.3
-
26
-
-
33745684683
-
Weighted and unweighted network of amino acids within protein
-
Aftabuddin, M.; Kundu, S. Weighted and unweighted network of amino acids within protein. Phys. A 2006, 369, 895-904.
-
(2006)
Phys. A
, vol.369
, pp. 895-904
-
-
Aftabuddin, M.1
Kundu, S.2
-
27
-
-
0029919190
-
Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading
-
Miyazawa, S.; Jernigan, R.L. Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading. J. Mol. Biol. 1996, 256, 623-644.
-
(1996)
J. Mol. Biol
, vol.256
, pp. 623-644
-
-
Miyazawa, S.1
Jernigan, R.L.2
-
28
-
-
34248185088
-
Construction and application of the weighted amino acid network based on energy
-
Jiao, X.; Chang, S.; Li, C.; Wang, C. Construction and application of the weighted amino acid network based on energy. Phys. Rev. E 2007, 75, 051903:1-051903:6.
-
(2007)
Phys. Rev. E
, vol.75
-
-
Jiao, X.1
Chang, S.2
Li, C.3
Wang, C.4
-
29
-
-
67749133760
-
Are the native states of proteins kinetic traps?
-
Cruzeiro, L.; Lopes, P.A. Are the native states of proteins kinetic traps? Mol. Phys. 2009, 107, 1485-1493.
-
(2009)
Mol. Phys
, vol.107
, pp. 1485-1493
-
-
Cruzeiro, L.1
Lopes, P.A.2
-
30
-
-
67650097331
-
Comparison of several molecular docking programs: Pose prediction and virtual screening accuracy
-
Cross, J.B.; Thompson, D.C.; Rai, B.K.; Baber, J.C.; Fan, K.Y.; Hu, Y.B.; Humblet, C. Comparison of several molecular docking programs: Pose prediction and virtual screening accuracy. J. Chem. Inf. Model. 2009, 49, 1455-1474.
-
(2009)
J. Chem. Inf. Model
, vol.49
, pp. 1455-1474
-
-
Cross, J.B.1
Thompson, D.C.2
Rai, B.K.3
Baber, J.C.4
Fan, K.Y.5
Hu, Y.B.6
Humblet, C.7
-
31
-
-
0038187615
-
A protein-protein docking benchmark
-
Chen, R.; Mintseris, J.; Janin, J.; Weng, Z. A protein-protein docking benchmark. Proteins: Struct. Funct. Bioinf. 2003, 52, 88-91.
-
(2003)
Proteins: Struct. Funct. Bioinf
, vol.52
, pp. 88-91
-
-
Chen, R.1
Mintseris, J.2
Janin, J.3
Weng, Z.4
-
32
-
-
10744226366
-
Rosetta predictions in CASP5: Successes, failures, and prospects for complete automation
-
Bradley, P.; Chivian, D.; Meiler, J.; Misura, K.; Rohl, C.A.; Schief, W.R.; Wedemeyer, W.J.; Schueler-Furman, O.; Murphy, P.; Schonbrun, J. Rosetta predictions in CASP5: Successes, failures, and prospects for complete automation. Proteins: Struct. Funct. Bioinf. 2003, 53, 457-468.
-
(2003)
Proteins: Struct. Funct. Bioinf
, vol.53
, pp. 457-468
-
-
Bradley, P.1
Chivian, D.2
Meiler, J.3
Misura, K.4
Rohl, C.A.5
Schief, W.R.6
Wedemeyer, W.J.7
Schueler-Furman, O.8
Murphy, P.9
Schonbrun, J.10
-
33
-
-
1642308591
-
The architecture of complex weighted networks
-
Barrat, A.; Barthelemy, M.; Pastor-Satorras, R.; Vespignani, A. The architecture of complex weighted networks. Proc. Natl. Acad. Sci. USA 2004, 101, 3747-3752.
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, pp. 3747-3752
-
-
Barrat, A.1
Barthelemy, M.2
Pastor-Satorras, R.3
Vespignani, A.4
-
34
-
-
9944264452
-
Characterization and modeling of weighted networks
-
Barthelemy, M.; Barrat, A.; Pastor-Satorras, R.; Vespignani, A. Characterization and modeling of weighted networks. Phys. A 2005, 346, 34-43.
-
(2005)
Phys. A
, vol.346
, pp. 34-43
-
-
Barthelemy, M.1
Barrat, A.2
Pastor-Satorras, R.3
Vespignani, A.4
-
35
-
-
0033562633
-
Use of pair potentials across protein interfaces in screening predicted docked complexes
-
Moont, G.; Gabb, H.A.; Sternberg, M.J.E. Use of pair potentials across protein interfaces in screening predicted docked complexes. Proteins: Struct. Funct. Bioinf. 1999, 35, 364-373.
-
(1999)
Proteins: Struct. Funct. Bioinf
, vol.35
, pp. 364-373
-
-
Moont, G.1
Gabb, H.A.2
Sternberg, M.J.E.3
|