-
1
-
-
0037453510
-
Assembly of cell regulatory systems through protein interaction domains
-
Pawson T, Nash P. Assembly of cell regulatory systems through protein interaction domains. Science 2003;300:445-452.
-
(2003)
Science
, vol.300
, pp. 445-452
-
-
Pawson, T.1
Nash, P.2
-
2
-
-
49549083915
-
Peptide-mediated interactions in biological systems: New discoveries and applications
-
Petsalaki E, Russell RB. Peptide-mediated interactions in biological systems: new discoveries and applications. Curr Opin Biotechnol 2008;19:344-350.
-
(2008)
Curr Opin Biotechnol
, vol.19
, pp. 344-350
-
-
Petsalaki, E.1
Russell, R.B.2
-
3
-
-
14644435825
-
Intrinsically unstructured proteins and their functions
-
Dyson HJ, Wright PE. Intrinsically unstructured proteins and their functions. Nat Rev Mol Cell Biol 2005;6:197-208.
-
(2005)
Nat Rev Mol Cell Biol
, vol.6
, pp. 197-208
-
-
Dyson, H.J.1
Wright, P.E.2
-
4
-
-
0036468397
-
Coupling of folding and binding for unstructured proteins
-
Dyson HJ, Wright PE. Coupling of folding and binding for unstructured proteins. Curr Opin Struct Biol 2002;12:54-60.
-
(2002)
Curr Opin Struct Biol
, vol.12
, pp. 54-60
-
-
Dyson, H.J.1
Wright, P.E.2
-
5
-
-
34250815165
-
Characterization of molecular recognition features Mo RFs, and their binding partners
-
Vacic V, Oldfield CJ, Mohan A, Radivojac P, Cortese MS, Uversky VN, Dunker AK. Characterization of molecular recognition features. Mo RFs, and their binding partners. J Proteome Res 2007;6:2351-2366.
-
(2007)
J Proteome Res
, vol.6
, pp. 2351-2366
-
-
Vacic, V.1
Oldfield, C.J.2
Mohan, A.3
Radivojac, P.4
Cortese, M.S.5
Uversky, V.N.6
Dunker, A.K.7
-
6
-
-
34249695447
-
Local structural disorder imparts plasticity on linear motifs
-
Fuxreiter M, Tompa P, Simon I. Local structural disorder imparts plasticity on linear motifs. Bioinformatics 2007;23:950-956.
-
(2007)
Bioinformatics
, vol.23
, pp. 950-956
-
-
Fuxreiter, M.1
Tompa, P.2
Simon, I.3
-
8
-
-
34347226332
-
Inhibiting HIV-1 integrase by shifting its oligomerization equilibrium
-
Hayouka Z, Rosenbluh J, Levin A, Loya S, Lebendiker M, Veprintsev D, Kotler M, Hizi A, Loyter A, Friedler A. Inhibiting HIV-1 integrase by shifting its oligomerization equilibrium. Proc Natl Acad Sci USA 2007;104:8316-8321.
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, pp. 8316-8321
-
-
Hayouka, Z.1
Rosenbluh, J.2
Levin, A.3
Loya, S.4
Lebendiker, M.5
Veprintsev, D.6
Kotler, M.7
Hizi, A.8
Loyter, A.9
Friedler, A.10
-
9
-
-
69949168453
-
A SPR strategy for high-throughput ligand screenings based on synthetic peptides mimicking a selected subdomain of the target protein: A proof of concept on HER2 receptor
-
Monfregola L, Vitale RM, Amodeo P, De Luca S. A SPR strategy for high-throughput ligand screenings based on synthetic peptides mimicking a selected subdomain of the target protein: a proof of concept on HER2 receptor. Bioorg Med Chem 2009;17:7015-7020.
-
(2009)
Bioorg Med Chem
, vol.17
, pp. 7015-7020
-
-
Monfregola, L.1
Vitale, R.M.2
Amodeo, P.3
De Luca, S.4
-
10
-
-
67349275522
-
Peptidic modulators of protein-protein interactions: Progress and challenges in computational design
-
Rubinstein M, Niv MY. Peptidic modulators of protein-protein interactions: progress and challenges in computational design. Biopolymers 2009;91:505-513.
-
(2009)
Biopolymers
, vol.91
, pp. 505-513
-
-
Rubinstein, M.1
Niv, M.Y.2
-
11
-
-
56449096489
-
Approved drug mimics of short peptide ligands from protein interaction motifs
-
Parthasarathi L, Casey F, Stein A, Aloy P, Shields DC. Approved drug mimics of short peptide ligands from protein interaction motifs. J Chem Inf Model 2008;48:1943-1948.
-
(2008)
J Chem Inf Model
, vol.48
, pp. 1943-1948
-
-
Parthasarathi, L.1
Casey, F.2
Stein, A.3
Aloy, P.4
Shields, D.C.5
-
12
-
-
65249171530
-
Design of protein-interaction specificity gives selective bZIP-binding peptides
-
Grigoryan G, Reinke AW, Keating AE. Design of protein-interaction specificity gives selective bZIP-binding peptides. Nature 2009;458: 859-864.
-
(2009)
Nature
, vol.458
, pp. 859-864
-
-
Grigoryan, G.1
Reinke, A.W.2
Keating, A.E.3
-
13
-
-
0026726041
-
Peptoids: A modular approach to drug discovery
-
Simon RJ, Kania RS, Zuckermann RN, Huebner VD, Jewell DA, Banville S, Ng S, Wang L, Rosenberg S, Marlowe CK, Spellmeyer DC, Tans R, Frankel AD, Santi DV, Cohen FE, Bartlett PA. Peptoids: a modular approach to drug discovery. Proc Natl Acad Sci USA 1992;89:9367-9371.
-
(1992)
Proc Natl Acad Sci USA
, vol.89
, pp. 9367-9371
-
-
Simon, R.J.1
Kania, R.S.2
Zuckermann, R.N.3
Huebner, V.D.4
Jewell, D.A.5
Banville, S.6
Ng, S.7
Wang, L.8
Rosenberg, S.9
Marlowe, C.K.10
Spellmeyer, D.C.11
Tans, R.12
Frankel, A.D.13
Santi, D.V.14
Cohen, F.E.15
Bartlett, P.A.16
-
14
-
-
18144394737
-
Design and structure of peptide and peptidomimetic antagonists of protein-protein interaction
-
Sillerud LO, Larson RS. Design and structure of peptide and peptidomimetic antagonists of protein-protein interaction. Curr Protein Pept Sci 2005;6:151-169.
-
(2005)
Curr Protein Pept Sci
, vol.6
, pp. 151-169
-
-
Sillerud, L.O.1
Larson, R.S.2
-
15
-
-
57549106061
-
Peptides as protein binding site mimetics
-
Eichler J. Peptides as protein binding site mimetics. Curr Opin Chem Biol 2008;12:707-713.
-
(2008)
Curr Opin Chem Biol
, vol.12
, pp. 707-713
-
-
Eichler, J.1
-
16
-
-
64549115839
-
Protein structure prediction: When is it useful?
-
Zhang Y. Protein structure prediction: when is it useful? Curr Opin Struct Biol 2009;19:145-155.
-
(2009)
Curr Opin Struct Biol
, vol.19
, pp. 145-155
-
-
Zhang, Y.1
-
17
-
-
64549106038
-
Convergence and combination of methods in protein-protein docking
-
Vajda S, Kozakov D. Convergence and combination of methods in protein-protein docking. Curr Opin Struct Biol 2009;19:164-170.
-
(2009)
Curr Opin Struct Biol
, vol.19
, pp. 164-170
-
-
Vajda, S.1
Kozakov, D.2
-
18
-
-
0037138380
-
Can we infer peptide recognition specificity mediated by SH3 domains?
-
Cesareni G, Panni S, Nardelli G, Castagnoli L. Can we infer peptide recognition specificity mediated by SH3 domains? FEBS Lett 2002; 513:38-44.
-
(2002)
FEBS Lett
, vol.513
, pp. 38-44
-
-
Cesareni, G.1
Panni, S.2
Nardelli, G.3
Castagnoli, L.4
-
19
-
-
26444604826
-
A flexible docking procedure for the exploration of peptide binding selectivity to known structures and homology models of PDZ domains
-
Niv MY, Weinstein H. A flexible docking procedure for the exploration of peptide binding selectivity to known structures and homology models of PDZ domains. J Am Chem Soc 2005;127:14072-14079.
-
(2005)
J Am Chem Soc
, vol.127
, pp. 14072-14079
-
-
Niv, M.Y.1
Weinstein, H.2
-
20
-
-
33646058599
-
Ab initio prediction of peptide-MHC binding geometry for diverse class i MHC allotypes
-
Bordner AJ, Abagyan R. Ab initio prediction of peptide-MHC binding geometry for diverse class I MHC allotypes. Proteins 2006;63: 512-526.
-
(2006)
Proteins
, vol.63
, pp. 512-526
-
-
Bordner, A.J.1
Abagyan, R.2
-
21
-
-
0030424581
-
Structure and function of the WW domain
-
1996
-
Sudol M. Structure and function of the WW domain. Prog Biophys Mol Biol 1996;65:113-132, 1996.
-
(1996)
Prog Biophys Mol Biol
, vol.65
, pp. 113-132
-
-
Sudol, M.1
-
22
-
-
15644379801
-
Recognition of unique carboxyl-terminal motifs by distinct PDZ domains
-
Songyang Z, Fanning AS, Fu C, Xu J, Marfatia SM, Chishti AH, Crompton A, Chan AC, Anderson JM, Cantley LC. Recognition of unique carboxyl-terminal motifs by distinct PDZ domains. Science 1997;275:73-77.
-
(1997)
Science
, vol.275
, pp. 73-77
-
-
Songyang, Z.1
Fanning, A.S.2
Fu, C.3
Xu, J.4
Marfatia, S.M.5
Chishti, A.H.6
Crompton, A.7
Chan, A.C.8
Anderson, J.M.9
Cantley, L.C.10
-
23
-
-
0026794581
-
The three-dimensional structure of HLA-B27 at 2.1 A resolution suggests a general mechanism for tight peptide binding to MHC
-
Madden DR, Gorga JC, Strominger JL, Wiley DC. The three-dimensional structure of HLA-B27 at 2.1 A resolution suggests a general mechanism for tight peptide binding to MHC. Cell 1992;70:1035-1048.
-
(1992)
Cell
, vol.70
, pp. 1035-1048
-
-
Madden, D.R.1
Gorga, J.C.2
Strominger, J.L.3
Wiley, D.C.4
-
24
-
-
0032428378
-
Identification of protein-protein interfaces by decreased amide proton solvent accessibility
-
Mandell JG, Falick AM, Komives EA. Identification of protein-protein interfaces by decreased amide proton solvent accessibility. Proc Natl Acad Sci USA 1998;95:14705-14710.
-
(1998)
Proc Natl Acad Sci USA
, vol.95
, pp. 14705-14710
-
-
Mandell, J.G.1
Falick, A.M.2
Komives, E.A.3
-
27
-
-
61449104961
-
Fragment-based identification of druggable hot spots of proteins using Fourier domain correlation techniques
-
Brenke R, Kozakov D, Chuang GY, Beglov D, Hall D, Landon MR, Mattos C, Vajda S. Fragment-based identification of druggable 'hot spots' of proteins using Fourier domain correlation techniques. Bioinformatics 2009;25:621-627.
-
(2009)
Bioinformatics
, vol.25
, pp. 621-627
-
-
Brenke, R.1
Kozakov, D.2
Chuang, G.Y.3
Beglov, D.4
Hall, D.5
Landon, M.R.6
Mattos, C.7
Vajda, S.8
-
28
-
-
74549149999
-
Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure
-
Capra JA, Laskowski RA, Thornton JM, Singh M, Funkhouser TA. Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure. PLoS Comput Biol 2009;5: e1000585.
-
(2009)
PLoS Comput Biol
, vol.5
-
-
Capra, J.A.1
Laskowski, R.A.2
Thornton, J.M.3
Singh, M.4
Funkhouser, T.A.5
-
29
-
-
72749083363
-
Interaction of the disordered yersinia effector protein YopE with its cognate chaperone SycE
-
Hu X, Lee MS, Wallqvist A. Interaction of the disordered Yersinia effector protein YopE with its cognate chaperone SycE. Biochemistry 2009;48:11158-11160.
-
(2009)
Biochemistry
, vol.48
, pp. 11158-11160
-
-
Hu, X.1
Lee, M.S.2
Wallqvist, A.3
-
30
-
-
33748276474
-
Protein-ligand docking: Current status and future challenges
-
Sousa SF, Fernandes PA, Ramos MJ. Protein-ligand docking: current status and future challenges. Proteins 2006;65:15-26.
-
(2006)
Proteins
, vol.65
, pp. 15-26
-
-
Sousa, S.F.1
Fernandes, P.A.2
Ramos, M.J.3
-
31
-
-
53249111802
-
A new peptide docking strategy using a mean field technique with mutually orthogonal Latin square sampling
-
Arun Prasad P, Gautham N. A new peptide docking strategy using a mean field technique with mutually orthogonal Latin square sampling. J Comput Aided Mol Des 2008;22:815-829.
-
(2008)
J Comput Aided Mol des
, vol.22
, pp. 815-829
-
-
Arun Prasad, P.1
Gautham, N.2
-
32
-
-
0036084259
-
Efficient docking of peptides to proteins without prior knowledge of the binding site
-
Hetenyi C, van der Spoel D. Efficient docking of peptides to proteins without prior knowledge of the binding site. Protein Sci 2002; 11:1729-1737.
-
(2002)
Protein Sci
, vol.11
, pp. 1729-1737
-
-
Hetenyi, C.1
Van Der Spoel, D.2
-
33
-
-
4344589929
-
Modeling the structure of bound peptide ligands to major histocompatibility complex
-
Tong JC, Tan TW, Ranganathan S. Modeling the structure of bound peptide ligands to major histocompatibility complex. Protein Sci 2004;13:2523-2532.
-
(2004)
Protein Sci
, vol.13
, pp. 2523-2532
-
-
Tong, J.C.1
Tan, T.W.2
Ranganathan, S.3
-
34
-
-
30744455459
-
Structural prediction of peptides bound to MHC class I
-
Fagerberg T, Cerottini JC, Michielin O. Structural prediction of peptides bound to MHC class I. J Mol Biol 2006;356:521-546.
-
(2006)
J Mol Biol
, vol.356
, pp. 521-546
-
-
Fagerberg, T.1
Cerottini, J.C.2
Michielin, O.3
-
35
-
-
70350010160
-
All-atom monte carlo approach to proteinpeptide binding
-
Staneva I, Wallin S. All-Atom Monte Carlo Approach to ProteinPeptide Binding. J Mol Biol 2009;393:1118-1128.
-
(2009)
J Mol Biol
, vol.393
, pp. 1118-1128
-
-
Staneva, I.1
Wallin, S.2
-
36
-
-
67349248904
-
Structure-based prediction of the Saccharomyces cerevisiae SH3-ligand interactions
-
Fernandez-Ballester G, Beltrao P, Gonzalez JM, Song YH, Wilmanns M, Valencia A, Serrano L. Structure-based prediction of the Saccharomyces cerevisiae SH3-ligand interactions. J Mol Biol 2009;388: 902-916.
-
(2009)
J Mol Biol
, vol.388
, pp. 902-916
-
-
Fernandez-Ballester, G.1
Beltrao, P.2
Gonzalez, J.M.3
Song, Y.H.4
Wilmanns, M.5
Valencia, A.6
Serrano, L.7
-
37
-
-
71049127018
-
Identification of structural mechanisms of HIV-1 protease specificity using computational peptide docking: Implications for drug resistance
-
Chaudhury S, Gray JJ. Identification of structural mechanisms of HIV-1 protease specificity using computational peptide docking: implications for drug resistance. Structure 2009;17:1636-1648.
-
(2009)
Structure
, vol.17
, pp. 1636-1648
-
-
Chaudhury, S.1
Gray, J.J.2
-
38
-
-
3142745414
-
Structural mining self-consistent design on flexible protein-peptide docking and transferable binding affinity potential
-
Liu Z, Dominy BN, Shakhnovich EI. Structural mining: self-consistent design on flexible protein-peptide docking and transferable binding affinity potential. J Am Chem Soc 2004;126:8515-8528.
-
(2004)
J Am Chem Soc
, vol.126
, pp. 8515-8528
-
-
Liu, Z.1
Dominy, B.N.2
Shakhnovich, E.I.3
-
39
-
-
77951223167
-
DynaDock: A new molecular dynamics-based algorithm for protein-peptide docking including receptor flexibility
-
Antes I. DynaDock: A new molecular dynamics-based algorithm for protein-peptide docking including receptor flexibility. Proteins 2010;78:1084-1104.
-
(2010)
Proteins
, vol.78
, pp. 1084-1104
-
-
Antes, I.1
-
40
-
-
50649095790
-
Macromolecular modeling with rosetta
-
Das R, Baker D. Macromolecular modeling with rosetta. Annu Rev Biochem 2008;77:363-382.
-
(2008)
Annu Rev Biochem
, vol.77
, pp. 363-382
-
-
Das, R.1
Baker, D.2
-
41
-
-
0023430366
-
Monte Carlo-minimization approach to the multiple-minima problem in protein folding
-
Li Z, Scheraga HA. Monte Carlo-minimization approach to the multiple-minima problem in protein folding. Proc Natl Acad Sci USA 1987;84:6611-6615.
-
(1987)
Proc Natl Acad Sci USA
, vol.84
, pp. 6611-6615
-
-
Li, Z.1
Scheraga, H.A.2
-
42
-
-
29144455315
-
Systematic discovery of new recognition peptides mediating protein interaction networks
-
Neduva V, Linding R, Su-Angrand I, Stark A, de Masi F, Gibson TJ, Lewis J, Serrano L, Russell RB. Systematic discovery of new recognition peptides mediating protein interaction networks. PLoS Biol 2005;3:e405.
-
(2005)
PLoS Biol
, vol.3
-
-
Neduva, V.1
Linding, R.2
Su-Angrand, I.3
Stark, A.4
De Masi, F.5
Gibson, T.J.6
Lewis, J.7
Serrano, L.8
Russell, R.B.9
-
43
-
-
0042622252
-
ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins
-
Puntervoll P, Linding R, Gemund C, Chabanis-Davidson S, Mattingsdal M, Cameron S, Martin DM, Ausiello G, Brannetti B, Costantini A, Ferre F, Maselli V, Via A, Cesareni G, Diella F, SupertiFurga G, Wyrwicz L, Ramu C, McGuigan C, Gudavalli R, Letunic I, Bork P, Rychlewski L, Kuster B, Helmer-Citterich M, Hunter WN, Aasland R, Gibson TJ. ELM server: a new resource for investigating short functional sites in modular eukaryotic proteins. Nucleic Acids Res 2003;31:3625-3630.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 3625-3630
-
-
Puntervoll, P.1
Linding, R.2
Gemund, C.3
Chabanis-Davidson, S.4
Mattingsdal, M.5
Cameron, S.6
Martin, D.M.7
Ausiello, G.8
Brannetti, B.9
Costantini, A.10
Ferre, F.11
Maselli, V.12
Via, A.13
Cesareni, G.14
Diella, F.15
SupertiFurga, G.16
Wyrwicz, L.17
Ramu, C.18
McGuigan, C.19
Gudavalli, R.20
Letunic, I.21
Bork, P.22
Rychlewski, L.23
Kuster, B.24
Helmer-Citterich, M.25
Hunter, W.N.26
Aasland, R.27
Gibson, T.J.28
more..
-
44
-
-
70349229596
-
Dynamic interactions of proteins in complex networks: A more structured view
-
Stein A, Pache RA, Bernado P, Pons M, Aloy P. Dynamic interactions of proteins in complex networks: a more structured view. FEBS J 2009;276:5390-5405.
-
(2009)
FEBS J
, vol.276
, pp. 5390-5405
-
-
Stein, A.1
Pache, R.A.2
Bernado, P.3
Pons, M.4
Aloy, P.5
-
45
-
-
0042710087
-
Computational alanine scanning to probe protein-protein interactions a novel approach to evaluate binding free energies
-
Massova I, Kollman PA. Computational alanine scanning to probe protein-protein interactions: a novel approach to evaluate binding free energies. J Am Chem Soc 1999;121:8133-8143.
-
(1999)
J Am Chem Soc
, vol.121
, pp. 8133-8143
-
-
Massova, I.1
Kollman, P.A.2
-
46
-
-
3242879771
-
Computational alanine scanning of protein-protein interfaces
-
Kortemme T, Kim DE, Baker D. Computational alanine scanning of protein-protein interfaces. Sci STKE 2004;2004:12.
-
(2004)
Sci STKE 2004
, pp. 12
-
-
Kortemme, T.1
Kim, D.E.2
Baker, D.3
-
47
-
-
0036291145
-
Predicting changes in the stability of proteins and protein complexes a study of more than 1000 mutations
-
Guerois R, Nielsen JE, Serrano L. Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations. J Mol Biol 2002;320:369-387.
-
(2002)
J Mol Biol
, vol.320
, pp. 369-387
-
-
Guerois, R.1
Nielsen, J.E.2
Serrano, L.3
-
49
-
-
0014592230
-
Computed circular dichroism spectra for the evaluation of protein conformation
-
Greenfield N, Fasman GD. Computed circular dichroism spectra for the evaluation of protein conformation. Biochemistry 1969;8:4108-4116.
-
(1969)
Biochemistry
, vol.8
, pp. 4108-4116
-
-
Greenfield, N.1
Fasman, G.D.2
-
50
-
-
45649084560
-
Backrub-like backbone simulation recapitulates natural protein conformational variability and improves mutant side-chain prediction
-
Smith CA, Kortemme T. Backrub-like backbone simulation recapitulates natural protein conformational variability and improves mutant side-chain prediction. J Mol Biol 2008;380:742-756.
-
(2008)
J Mol Biol
, vol.380
, pp. 742-756
-
-
Smith, C.A.1
Kortemme, T.2
-
51
-
-
0037406075
-
Cyclic coordinate descent: A robotics algorithm for protein loop closure
-
Canutescu AA, Dunbrack RL, Jr. Cyclic coordinate descent: a robotics algorithm for protein loop closure. Protein Sci 2003;12:963-972.
-
(2003)
Protein Sci
, vol.12
, pp. 963-972
-
-
Canutescu, A.A.1
Dunbrack Jr., R.L.2
-
52
-
-
68349104348
-
Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling
-
Mandell DJ, Coutsias EA, Kortemme T. Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling. Nat Methods 2009;6:551-552.
-
(2009)
Nat Methods
, vol.6
, pp. 551-552
-
-
Mandell, D.J.1
Coutsias, E.A.2
Kortemme, T.3
-
53
-
-
68149138672
-
Protein-peptide interactions adopt the same structural motifs as monomeric protein folds
-
Vanhee P, Stricher F, Baeten L, Verschueren E, Lenaerts T, Serrano L, Rousseau F, Schymkowitz J. Protein-peptide interactions adopt the same structural motifs as monomeric protein folds. Structure 2009;17:1128-1136.
-
(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
-
54
-
-
76649139794
-
Computational approaches to identifying and characterizing protein binding sites for ligand design
-
Henrich S, Salo-Ahen OM, Huang B, Rippmann FF, Cruciani G, Wade RC. Computational approaches to identifying and characterizing protein binding sites for ligand design. J Mol Recognit 2009;23:209-219.
-
(2009)
J Mol Recognit
, vol.23
, pp. 209-219
-
-
Henrich, S.1
Salo-Ahen, O.M.2
Huang, B.3
Rippmann, F.F.4
Cruciani, G.5
Wade, R.C.6
-
55
-
-
1842326139
-
Bayesian statistical analysis of protein side-chain rotamer preferences
-
Dunbrack RL, Jr., Cohen FE. Bayesian statistical analysis of protein side-chain rotamer preferences. Protein Sci 1997;6:1661-1681.
-
(1997)
Protein Sci
, vol.6
, pp. 1661-1681
-
-
Dunbrack Jr., R.L.1
Cohen, F.E.2
-
56
-
-
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
-
57
-
-
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
-
58
-
-
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
-
59
-
-
84964389892
-
Variable metric method for minimization
-
Davidon WC. Variable metric method for minimization. SIAM, Journal on Optim 1991;1:1-17.
-
(1991)
SIAM Journal on Optim
, vol.1
, pp. 1-17
-
-
Davidon, W.C.1
-
60
-
-
0034641749
-
Native protein sequences are close to optimal for their structures
-
Kuhlman. B, Baker D. Native protein sequences are close to optimal for their structures. Proc Natl Acad Sci USA 2000;97:10383-10388.
-
(2000)
Proc Natl Acad Sci USA
, vol.97
, pp. 10383-10388
-
-
Kuhlman, B.1
Baker, D.2
-
62
-
-
0029619259
-
Knowledge-based protein secondary structure assignment
-
Frishman D, Argos P. Knowledge-based protein secondary structure assignment. Proteins 1995;23:566-579.
-
(1995)
Proteins
, vol.23
, pp. 566-579
-
-
Frishman, D.1
Argos, P.2
-
63
-
-
1642540577
-
Evaluation of docking performance comparative data on docking algorithms
-
Kontoyianni M, McClellan LM, Sokol GS. Evaluation of docking performance: comparative data on docking algorithms. J Med Chem 2004;47:558-565.
-
(2004)
J Med Chem
, vol.47
, pp. 558-565
-
-
Kontoyianni, M.1
McClellan, L.M.2
Sokol, G.S.3
-
64
-
-
0033670439
-
MaxSub: An automated measure for the assessment of protein structure prediction quality
-
Siew N, Elofsson A, Rychlewski L, Fischer D. MaxSub: an automated measure for the assessment of protein structure prediction quality. Bioinformatics 2000;16:776-785.
-
(2000)
Bioinformatics
, vol.16
, pp. 776-785
-
-
Siew, N.1
Elofsson, A.2
Rychlewski, L.3
Fischer, D.4
|