-
1
-
-
77951223167
-
DynaDock: A new molecular dynamics-based algorithm for protein-peptide docking including receptor flexibility
-
I. Antes DynaDock: A new molecular dynamics-based algorithm for protein-peptide docking including receptor flexibility Proteins 78 2010 1084 1104
-
(2010)
Proteins
, vol.78
, pp. 1084-1104
-
-
Antes, I.1
-
2
-
-
45149114391
-
Reconstruction of protein backbones from the BriX collection of canonical protein fragments
-
L. Baeten, J. Reumers, V. Tur, F. Stricher, T. Lenaerts, L. Serrano, F. Rousseau, and J. Schymkowitz Reconstruction of protein backbones from the BriX collection of canonical protein fragments PLoS Comput. Biol. 4 2008 e1000083
-
(2008)
PLoS Comput. Biol.
, vol.4
, pp. 1000083
-
-
Baeten, L.1
Reumers, J.2
Tur, V.3
Stricher, F.4
Lenaerts, T.5
Serrano, L.6
Rousseau, F.7
Schymkowitz, J.8
-
3
-
-
77954481626
-
Prediction of protease substrates using sequence and structure features
-
D.T. Barkan, D.R. Hostetter, S. Mahrus, U. Pieper, J.A. Wells, C.S. Craik, and A. Sali Prediction of protease substrates using sequence and structure features Bioinformatics 26 2010 1714 1722
-
(2010)
Bioinformatics
, vol.26
, pp. 1714-1722
-
-
Barkan, D.T.1
Hostetter, D.R.2
Mahrus, S.3
Pieper, U.4
Wells, J.A.5
Craik, C.S.6
Sali, A.7
-
4
-
-
82955168441
-
Structural and dynamic determinants of protein-peptide recognition
-
O. Dagliyan, E.A. Proctor, K.M. D'Auria, F. Ding, and N.V. Dokholyan Structural and dynamic determinants of protein-peptide recognition Structure 19 2011 1837 1845
-
(2011)
Structure
, vol.19
, pp. 1837-1845
-
-
Dagliyan, O.1
Proctor, E.A.2
D'Auria, K.M.3
Ding, F.4
Dokholyan, N.V.5
-
5
-
-
77957237749
-
Rapid flexible docking using a stochastic rotamer library of ligands
-
F. Ding, S. Yin, and N.V. Dokholyan Rapid flexible docking using a stochastic rotamer library of ligands J. Chem. Inf. Model. 50 2010 1623 1632
-
(2010)
J. Chem. Inf. Model.
, vol.50
, pp. 1623-1632
-
-
Ding, F.1
Yin, S.2
Dokholyan, N.V.3
-
6
-
-
0036084259
-
Efficient docking of peptides to proteins without prior knowledge of the binding site
-
C. Hetényi, and D. van der Spoel Efficient docking of peptides to proteins without prior knowledge of the binding site Protein Sci. 11 2002 1729 1737
-
(2002)
Protein Sci.
, vol.11
, pp. 1729-1737
-
-
Hetényi, C.1
Van Der Spoel, D.2
-
7
-
-
0002514541
-
Algorithms for constraint-satisfaction problems: A survey
-
V. Kumar Algorithms for Constraint-Satisfaction Problems: A Survey AI Mag. 13 1992 32
-
(1992)
AI Mag.
, vol.13
, pp. 32
-
-
Kumar, V.1
-
9
-
-
0038021436
-
Assessment of blind predictions of protein-protein interactions: Current status of docking methods
-
R. Méndez, R. Leplae, L. De Maria, and S.J. Wodak Assessment of blind predictions of protein-protein interactions: current status of docking methods Proteins 52 2003 51 67
-
(2003)
Proteins
, vol.52
, pp. 51-67
-
-
Méndez, R.1
Leplae, R.2
De Maria, L.3
Wodak, S.J.4
-
10
-
-
49549083915
-
Peptide-mediated interactions in biological systems: New discoveries and applications
-
E. Petsalaki, and R.B. Russell Peptide-mediated interactions in biological systems: new discoveries and applications Curr. Opin. Biotechnol. 19 2008 344 350
-
(2008)
Curr. Opin. Biotechnol.
, vol.19
, pp. 344-350
-
-
Petsalaki, E.1
Russell, R.B.2
-
12
-
-
4444221565
-
UCSF Chimera - A visualization system for exploratory research and analysis
-
E.F. Pettersen, T.D. Goddard, C.C. Huang, G.S. Couch, D.M. Greenblatt, E.C. Meng, and T.E. Ferrin UCSF Chimera - a visualization system for exploratory research and analysis J. Comput. Chem. 25 2004 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
-
13
-
-
77953573815
-
Sub-angstrom modeling of complexes between flexible peptides and globular proteins
-
B. Raveh, N. London, and O. Schueler-Furman Sub-angstrom modeling of complexes between flexible peptides and globular proteins Proteins 78 2010 2029 2040
-
(2010)
Proteins
, vol.78
, pp. 2029-2040
-
-
Raveh, B.1
London, N.2
Schueler-Furman, O.3
-
14
-
-
84864579478
-
Domain-mediated protein interaction prediction: From genome to network
-
J. Reimand, S. Hui, S. Jain, B. Law, and G.D. Bader Domain-mediated protein interaction prediction: From genome to network FEBS Lett. 586 2012 2751 2763
-
(2012)
FEBS Lett.
, vol.586
, pp. 2751-2763
-
-
Reimand, J.1
Hui, S.2
Jain, S.3
Law, B.4
Bader, G.D.5
-
15
-
-
41149178980
-
A careful disorderliness in the proteome: Sites for interaction and targets for future therapies
-
R.B. Russell, and T.J. Gibson A careful disorderliness in the proteome: sites for interaction and targets for future therapies FEBS Lett. 582 2008 1271 1275
-
(2008)
FEBS Lett.
, vol.582
, pp. 1271-1275
-
-
Russell, R.B.1
Gibson, T.J.2
-
16
-
-
0030040323
-
Reduced surface: An efficient way to compute molecular surfaces
-
M.F. Sanner, A.J. Olson, and J.C. Spehner Reduced surface: an efficient way to compute molecular surfaces Biopolymers 38 1996 305 320
-
(1996)
Biopolymers
, vol.38
, pp. 305-320
-
-
Sanner, M.F.1
Olson, A.J.2
Spehner, J.C.3
-
17
-
-
0033820208
-
Structure-based prediction of binding peptides to MHC class i molecules: Application to a broad range of MHC alleles
-
O. Schueler-Furman, Y. Altuvia, A. Sette, and H. Margalit Structure-based prediction of binding peptides to MHC class I molecules: application to a broad range of MHC alleles Protein Sci. 9 2000 1838 1846
-
(2000)
Protein Sci.
, vol.9
, pp. 1838-1846
-
-
Schueler-Furman, O.1
Altuvia, Y.2
Sette, A.3
Margalit, H.4
-
18
-
-
23144436398
-
The FoldX web server: An online force field
-
WEB SERVER ISSUE W382-8
-
J. Schymkowitz, J. Borg, F. Stricher, R. Nys, F. Rousseau, and L. Serrano The FoldX web server: an online force field Nucleic Acids Res. 33 Web Server issue 2005 W382-8
-
(2005)
Nucleic Acids Res.
, vol.33
-
-
Schymkowitz, J.1
Borg, J.2
Stricher, F.3
Nys, R.4
Rousseau, F.5
Serrano, L.6
-
19
-
-
0032446607
-
The structural basis of estrogen receptor/coactivator recognition and the antagonism of this interaction by tamoxifen
-
A.K. Shiau, D. Barstad, P.M. Loria, L. Cheng, P.J. Kushner, D.A. Agard, and G.L. Greene The structural basis of estrogen receptor/coactivator recognition and the antagonism of this interaction by tamoxifen Cell 95 1998 927 937
-
(1998)
Cell
, vol.95
, pp. 927-937
-
-
Shiau, A.K.1
Barstad, D.2
Loria, P.M.3
Cheng, L.4
Kushner, P.J.5
Agard, D.A.6
Greene, G.L.7
-
20
-
-
77955476975
-
Novel peptide-mediated interactions derived from high-resolution 3-dimensional structures
-
A. Stein, and P. Aloy Novel peptide-mediated interactions derived from high-resolution 3-dimensional structures PLoS Comput. Biol. 6 2010 e1000789
-
(2010)
PLoS Comput. Biol.
, vol.6
, pp. 1000789
-
-
Stein, A.1
Aloy, P.2
-
21
-
-
79953071469
-
Three-dimensional modeling of protein interactions and complexes is going 'omics
-
A. Stein, R. Mosca, and P. Aloy Three-dimensional modeling of protein interactions and complexes is going 'omics Curr. Opin. Struct. Biol. 21 2011 200 208
-
(2011)
Curr. Opin. Struct. Biol.
, vol.21
, pp. 200-208
-
-
Stein, A.1
Mosca, R.2
Aloy, P.3
-
22
-
-
34547127612
-
PDZ domain binding selectivity is optimized across the mouse proteome
-
M.A. Stiffler, J.R. Chen, V.P. Grantcharova, Y. Lei, D. Fuchs, J.E. Allen, L.A. Zaslavskaia, and G. MacBeath PDZ domain binding selectivity is optimized across the mouse proteome Science 317 2007 364 369
-
(2007)
Science
, vol.317
, pp. 364-369
-
-
Stiffler, M.A.1
Chen, J.R.2
Grantcharova, V.P.3
Lei, Y.4
Fuchs, D.5
Allen, J.E.6
Zaslavskaia, L.A.7
Macbeath, G.8
-
23
-
-
0037059461
-
A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules
-
A.H.Y. Tong, B. Drees, G. Nardelli, G.D. Bader, B. Brannetti, L. Castagnoli, M. Evangelista, S. Ferracuti, B. Nelson, and S. Paoluzi A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules Science 295 2002 321 324
-
(2002)
Science
, vol.295
, pp. 321-324
-
-
Tong, A.H.Y.1
Drees, B.2
Nardelli, G.3
Bader, G.D.4
Brannetti, B.5
Castagnoli, L.6
Evangelista, M.7
Ferracuti, S.8
Nelson, B.9
Paoluzi, S.10
-
24
-
-
70350404403
-
Bayesian modeling of the yeast SH3 domain interactome predicts spatiotemporal dynamics of endocytosis proteins
-
R. Tonikian, X. Xin, C.P. Toret, D. Gfeller, C. Landgraf, S. Panni, S. Paoluzi, L. Castagnoli, B. Currell, and S. Seshagiri Bayesian modeling of the yeast SH3 domain interactome predicts spatiotemporal dynamics of endocytosis proteins PLoS Biol. 7 2009 e1000218
-
(2009)
PLoS Biol.
, vol.7
, pp. 1000218
-
-
Tonikian, R.1
Xin, X.2
Toret, C.P.3
Gfeller, D.4
Landgraf, C.5
Panni, S.6
Paoluzi, S.7
Castagnoli, L.8
Currell, B.9
Seshagiri, S.10
-
25
-
-
84864419151
-
PepSite: Prediction of peptide-binding sites from protein surfaces
-
WEB SERVER ISSUE W423-7
-
L.G. Trabuco, S. Lise, E. Petsalaki, and R.B. Russell PepSite: prediction of peptide-binding sites from protein surfaces Nucleic Acids Res. 40 Web Server issue 2012 W423-7
-
(2012)
Nucleic Acids Res.
, vol.40
-
-
Trabuco, L.G.1
Lise, S.2
Petsalaki, E.3
Russell, R.B.4
-
26
-
-
77954294794
-
HotPoint: Hot spot prediction server for protein interfaces
-
WEB SERVER ISSUE W402-6
-
N. Tuncbag, O. Keskin, and A. Gursoy HotPoint: hot spot prediction server for protein interfaces Nucleic Acids Res. 38 Web Server issue 2010 W402-6
-
(2010)
Nucleic Acids Res.
, vol.38
-
-
Tuncbag, N.1
Keskin, O.2
Gursoy, A.3
-
27
-
-
77955234902
-
VitAL: Viterbi algorithm for de novo peptide design
-
E.B. Unal, A. Gursoy, and B. Erman VitAL: Viterbi algorithm for de novo peptide design PLoS ONE 5 2010 e10926
-
(2010)
PLoS ONE
, vol.5
, pp. 10926
-
-
Unal, E.B.1
Gursoy, A.2
Erman, B.3
-
28
-
-
68149138672
-
Protein-peptide interactions adopt the same structural motifs as monomeric protein folds
-
P. Vanhee, F. Stricher, L. Baeten, E. Verschueren, T. Lenaerts, L. Serrano, F. Rousseau, and J. Schymkowitz Protein-peptide interactions adopt the same structural motifs as monomeric protein folds Structure 17 2009 1128 1136
-
(2009)
Structure
, vol.17
, pp. 1128-1136
-
-
Vanhee, P.1
Stricher, F.2
Baeten, L.3
Verschueren, E.4
Lenaerts, T.5
Serrano, L.6
Rousseau, F.7
Schymkowitz, J.8
-
29
-
-
79954780449
-
Computational design of peptide ligands
-
P. Vanhee, A.M. van der Sloot, E. Verschueren, L. Serrano, F. Rousseau, and J. Schymkowitz Computational design of peptide ligands Trends Biotechnol. 29 2011 231 239
-
(2011)
Trends Biotechnol.
, vol.29
, pp. 231-239
-
-
Vanhee, P.1
Van Der Sloot, A.M.2
Verschueren, E.3
Serrano, L.4
Rousseau, F.5
Schymkowitz, J.6
-
30
-
-
78651330862
-
BriX: A database of protein building blocks for structural analysis, modeling and design
-
DATABASE ISSUE
-
P. Vanhee, E. Verschueren, L. Baeten, F. Stricher, L. Serrano, F. Rousseau, and J. Schymkowitz BriX: a database of protein building blocks for structural analysis, modeling and design Nucleic Acids Res. 39 Database issue 2011 D435 D442
-
(2011)
Nucleic Acids Res.
, vol.39
-
-
Vanhee, P.1
Verschueren, E.2
Baeten, L.3
Stricher, F.4
Serrano, L.5
Rousseau, F.6
Schymkowitz, J.7
-
31
-
-
0025398721
-
WHAT IF: A molecular modeling and drug design program
-
29
-
G. Vriend WHAT IF: a molecular modeling and drug design program J. Mol. Graph. 8 1990 52 56 29
-
(1990)
J. Mol. Graph.
, vol.8
, pp. 52-56
-
-
Vriend, G.1
-
32
-
-
32344448382
-
Screening for peptide drugs from the natural repertoire of biodiverse protein folds
-
P.M. Watt Screening for peptide drugs from the natural repertoire of biodiverse protein folds Nat. Biotechnol. 24 2006 177 183
-
(2006)
Nat. Biotechnol.
, vol.24
, pp. 177-183
-
-
Watt, P.M.1
|