-
1
-
-
33646472024
-
High-resolution protein-protein docking
-
Gray J.J. High-resolution protein-protein docking. Curr. Opin. Struct. Biol. 16 (2006) 183-193
-
(2006)
Curr. Opin. Struct. Biol.
, vol.16
, pp. 183-193
-
-
Gray, J.J.1
-
2
-
-
0032897494
-
An analysis of conformational changes on protein-protein association: implications for predictive docking
-
Betts M.J., and Sternberg M.J. An analysis of conformational changes on protein-protein association: implications for predictive docking. Protein Eng. 12 (1999) 271-283
-
(1999)
Protein Eng.
, vol.12
, pp. 271-283
-
-
Betts, M.J.1
Sternberg, M.J.2
-
3
-
-
0003187567
-
The atomic structure of protein-protein recognition sites
-
Lo Conte L., Chothia C., and Janin J. The atomic structure of protein-protein recognition sites. J. Mol. Biol. 285 (1999) 2177-2198
-
(1999)
J. Mol. Biol.
, vol.285
, pp. 2177-2198
-
-
Lo Conte, L.1
Chothia, C.2
Janin, J.3
-
4
-
-
33645961330
-
Flexible protein-protein docking
-
Bonvin A.M. Flexible protein-protein docking. Curr. Opin. Struct. Biol. 16 (2006) 194-200
-
(2006)
Curr. Opin. Struct. Biol.
, vol.16
, pp. 194-200
-
-
Bonvin, A.M.1
-
5
-
-
84892166712
-
Einfluss der Configuration auf die Wirkung der Enzyme
-
Fischer E. Einfluss der Configuration auf die Wirkung der Enzyme. Ber. Dtsch. Chem. Ges. 27 (1894) 2985-2993
-
(1894)
Ber. Dtsch. Chem. Ges.
, vol.27
, pp. 2985-2993
-
-
Fischer, E.1
-
6
-
-
0018165127
-
Computer analysis of protein-protein interaction
-
Wodak S.J., and Janin J. Computer analysis of protein-protein interaction. J. Mol. Biol. 124 (1978) 323-342
-
(1978)
J. Mol. Biol.
, vol.124
, pp. 323-342
-
-
Wodak, S.J.1
Janin, J.2
-
7
-
-
0026572775
-
Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques
-
Katchalski-Katzir E., Shariv I., Eisenstein M., Friesem A.A., Aflalo C., and Vakser I.A. Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques. Proc. Natl Acad. Sci. USA 89 (1992) 2195-2199
-
(1992)
Proc. Natl Acad. Sci. USA
, vol.89
, pp. 2195-2199
-
-
Katchalski-Katzir, E.1
Shariv, I.2
Eisenstein, M.3
Friesem, A.A.4
Aflalo, C.5
Vakser, I.A.6
-
8
-
-
0038526303
-
ZDOCK: an initial-stage protein-docking algorithm
-
Chen R., Li L., and Weng Z. ZDOCK: an initial-stage protein-docking algorithm. Proteins 52 (2003) 80-87
-
(2003)
Proteins
, vol.52
, pp. 80-87
-
-
Chen, R.1
Li, L.2
Weng, Z.3
-
9
-
-
0242299200
-
RDOCK: refinement of rigid-body protein docking predictions
-
Li L., Chen R., and Weng Z. RDOCK: refinement of rigid-body protein docking predictions. Proteins 53 (2003) 693-707
-
(2003)
Proteins
, vol.53
, pp. 693-707
-
-
Li, L.1
Chen, R.2
Weng, Z.3
-
10
-
-
0345832301
-
ClusPro: an automated docking and discrimination method for the prediction of protein complexes
-
Comeau S.R., Gatchell D.W., Vajda S., and Camacho C.J. ClusPro: an automated docking and discrimination method for the prediction of protein complexes. Bioinformatics 20 (2004) 45-50
-
(2004)
Bioinformatics
, vol.20
, pp. 45-50
-
-
Comeau, S.R.1
Gatchell, D.W.2
Vajda, S.3
Camacho, C.J.4
-
11
-
-
0038161052
-
Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations
-
Gray J.J., Moughon S., Wang C., Schueler-Furman O., Kuhlman B., Rohl C.A., and Baker D. Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. J. Mol. Biol. 331 (2003) 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
-
12
-
-
21644458102
-
Classification of protein complexes based on docking difficulty
-
Vajda S. Classification of protein complexes based on docking difficulty. Proteins 60 (2005) 176-180
-
(2005)
Proteins
, vol.60
, pp. 176-180
-
-
Vajda, S.1
-
13
-
-
0021871375
-
A computational procedure for determining energetically favorable binding sites on biologically important macromolecules
-
Goodford P.J. A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. J. Med. Chem. 28 (1985) 849-857
-
(1985)
J. Med. Chem.
, vol.28
, pp. 849-857
-
-
Goodford, P.J.1
-
14
-
-
0020491251
-
A geometric approach to macromolecule-ligand interactions
-
Kuntz I.D., Blaney J.M., Oatley S.J., Langridge R., and Ferrin T.E. A geometric approach to macromolecule-ligand interactions. J. Mol. Biol. 161 (1982) 269-288
-
(1982)
J. Mol. Biol.
, vol.161
, pp. 269-288
-
-
Kuntz, I.D.1
Blaney, J.M.2
Oatley, S.J.3
Langridge, R.4
Ferrin, T.E.5
-
15
-
-
78651189765
-
On the nature of allosteric transitions: a plausible model
-
Monod J., Wyman J., and Changeux J.P. On the nature of allosteric transitions: a plausible model. J. Mol. Biol. 12 (1965) 88-118
-
(1965)
J. Mol. Biol.
, vol.12
, pp. 88-118
-
-
Monod, J.1
Wyman, J.2
Changeux, J.P.3
-
16
-
-
0033970020
-
Folding and binding cascades: dynamic landscapes and population shifts
-
Kumar S., Ma B., Tsai C.J., Sinha N., and Nussinov R. Folding and binding cascades: dynamic landscapes and population shifts. Protein Sci. 9 (2000) 10-19
-
(2000)
Protein Sci.
, vol.9
, pp. 10-19
-
-
Kumar, S.1
Ma, B.2
Tsai, C.J.3
Sinha, N.4
Nussinov, R.5
-
17
-
-
36749057349
-
Implicit flexibility in protein docking: cross-docking and local refinement
-
Krol M., Chaleil R.A., Tournier A.L., and Bates P.A. Implicit flexibility in protein docking: cross-docking and local refinement. Proteins 69 (2007) 7
-
(2007)
Proteins
, vol.69
, pp. 7
-
-
Krol, M.1
Chaleil, R.A.2
Tournier, A.L.3
Bates, P.A.4
-
18
-
-
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 G.R., Sternberg M.J., and Bates P.A. 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. 347 (2005) 1077-1101
-
(2005)
J. Mol. Biol.
, vol.347
, pp. 1077-1101
-
-
Smith, G.R.1
Sternberg, M.J.2
Bates, P.A.3
-
19
-
-
9944237833
-
Complementarity of structure ensembles in protein-protein binding
-
Grunberg R., Leckner J., and Nilges M. Complementarity of structure ensembles in protein-protein binding. Structure 12 (2004) 2125-2136
-
(2004)
Structure
, vol.12
, pp. 2125-2136
-
-
Grunberg, R.1
Leckner, J.2
Nilges, M.3
-
20
-
-
33644843079
-
Accounting for loop flexibility during protein-protein docking
-
Bastard K., Prevost C., and Zacharias M. Accounting for loop flexibility during protein-protein docking. Proteins 62 (2006) 956-969
-
(2006)
Proteins
, vol.62
, pp. 956-969
-
-
Bastard, K.1
Prevost, C.2
Zacharias, M.3
-
21
-
-
0001858251
-
Application of a theory of enzyme specificity to protein synthesis
-
Koshland D.E. Application of a theory of enzyme specificity to protein synthesis. Proc. Natl Acad. Sci. USA 44 (1958) 98-104
-
(1958)
Proc. Natl Acad. Sci. USA
, vol.44
, pp. 98-104
-
-
Koshland, D.E.1
-
22
-
-
0037442962
-
HADDOCK: a protein-protein docking approach based on biochemical or biophysical information
-
Dominguez C., Boelens R., and Bonvin A.M. HADDOCK: a protein-protein docking approach based on biochemical or biophysical information. J. Am. Chem. Soc. 125 (2003) 1731-1737
-
(2003)
J. Am. Chem. Soc.
, vol.125
, pp. 1731-1737
-
-
Dominguez, C.1
Boelens, R.2
Bonvin, A.M.3
-
23
-
-
34249884544
-
Flexible relaxation of rigid-body docking solutions
-
Krol M., Tournier A.L., and Bates P.A. Flexible relaxation of rigid-body docking solutions. Proteins 68 (2007) 159-169
-
(2007)
Proteins
, vol.68
, pp. 159-169
-
-
Krol, M.1
Tournier, A.L.2
Bates, P.A.3
-
24
-
-
21644477228
-
Incorporation of flexibility into rigid-body docking: applications in rounds 3-5 of CAPRI
-
Smith G.R., Fitzjohn P.W., Page C.S., and Bates P.A. Incorporation of flexibility into rigid-body docking: applications in rounds 3-5 of CAPRI. Proteins 60 (2005) 263-268
-
(2005)
Proteins
, vol.60
, pp. 263-268
-
-
Smith, G.R.1
Fitzjohn, P.W.2
Page, C.S.3
Bates, P.A.4
-
25
-
-
36748998784
-
HADDOCK versus HADDOCK: new features and performance of HADDOCK2.0 on the CAPRI targets
-
de Vries S.J., van Dijk A.D., Krzeminski M., van Dijk M., Thureau A., Hsu V., et al. HADDOCK versus HADDOCK: new features and performance of HADDOCK2.0 on the CAPRI targets. Proteins 69 (2007) 726-733
-
(2007)
Proteins
, vol.69
, pp. 726-733
-
-
de Vries, S.J.1
van Dijk, A.D.2
Krzeminski, M.3
van Dijk, M.4
Thureau, A.5
Hsu, V.6
-
26
-
-
34548861782
-
Protein-protein docking with backbone flexibility
-
Wang C., Bradley P., and Baker D. Protein-protein docking with backbone flexibility. J. Mol. Biol. 373 (2007) 503-519
-
(2007)
J. Mol. Biol.
, vol.373
, pp. 503-519
-
-
Wang, C.1
Bradley, P.2
Baker, D.3
-
27
-
-
36749075510
-
Incorporating biochemical information and backbone flexibility in RosettaDock for CAPRI rounds 6-12
-
Chaudhury S., Sircar A., Sivasubramanian A., Berrondo M., and Gray J.J. Incorporating biochemical information and backbone flexibility in RosettaDock for CAPRI rounds 6-12. Proteins 69 (2007) 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
-
28
-
-
36749066580
-
RosettaDock in CAPRI rounds 6-12
-
Wang C., Schueler-Furman O., Andre I., London N., Fleishman S.J., Bradley P., et al. RosettaDock in CAPRI rounds 6-12. Proteins 69 (2007) 758-763
-
(2007)
Proteins
, vol.69
, pp. 758-763
-
-
Wang, C.1
Schueler-Furman, O.2
Andre, I.3
London, N.4
Fleishman, S.J.5
Bradley, P.6
-
29
-
-
21644454184
-
Data-driven docking: HADDOCK's adventures in CAPRI
-
van Dijk A.D., de Vries S.J., Dominguez C., Chen H., Zhou H.X., and Bonvin A.M. Data-driven docking: HADDOCK's adventures in CAPRI. Proteins 60 (2005) 232-238
-
(2005)
Proteins
, vol.60
, pp. 232-238
-
-
van Dijk, A.D.1
de Vries, S.J.2
Dominguez, C.3
Chen, H.4
Zhou, H.X.5
Bonvin, A.M.6
-
30
-
-
1842607157
-
Structural model of the UbcH5B/CNOT4 complex revealed by combining NMR, mutagenesis, and docking approaches
-
Dominguez C., Bonvin A.M., Winkler G.S., van Schaik F.M.A., Timmersm H.T.M., and Boelens R. Structural model of the UbcH5B/CNOT4 complex revealed by combining NMR, mutagenesis, and docking approaches. Structure 12 (2004) 633-644
-
(2004)
Structure
, vol.12
, pp. 633-644
-
-
Dominguez, C.1
Bonvin, A.M.2
Winkler, G.S.3
van Schaik, F.M.A.4
Timmersm, H.T.M.5
Boelens, R.6
-
31
-
-
33748317827
-
Binding site structure f LRP-RAP complex: implications for a common ligand-receptor binding motif
-
Jensen G.A., Andersern O.M., Bonvin A.M., Bjerrum-Bohr I., Etzerodt M., Thogersen H.C., et al. Binding site structure f LRP-RAP complex: implications for a common ligand-receptor binding motif. J. Mol. Biol. 362 (2006) 700-716
-
(2006)
J. Mol. Biol.
, vol.362
, pp. 700-716
-
-
Jensen, G.A.1
Andersern, O.M.2
Bonvin, A.M.3
Bjerrum-Bohr, I.4
Etzerodt, M.5
Thogersen, H.C.6
-
33
-
-
0033167995
-
Exploring the dynamic information content of a protein NMR structure: comparison of a molecular dynamics simulation with the NMR and X-ray structures of Escherichia coli ribonuclease HI
-
Philippopoulos M., and Lim C. Exploring the dynamic information content of a protein NMR structure: comparison of a molecular dynamics simulation with the NMR and X-ray structures of Escherichia coli ribonuclease HI. Proteins 36 (1999) 87-110
-
(1999)
Proteins
, vol.36
, pp. 87-110
-
-
Philippopoulos, M.1
Lim, C.2
-
34
-
-
0038697805
-
Protein-protein docking predictions for the CAPRI experiment
-
Gray J.J., Moughon S.E., Kortemme T., Schueler-Furman O., Misura K.M., Morozov A.V., and Baker D. Protein-protein docking predictions for the CAPRI experiment. Proteins 52 (2003) 118-122
-
(2003)
Proteins
, vol.52
, pp. 118-122
-
-
Gray, J.J.1
Moughon, S.E.2
Kortemme, T.3
Schueler-Furman, O.4
Misura, K.M.5
Morozov, A.V.6
Baker, D.7
-
35
-
-
21644489506
-
CAPRI rounds 3-5 reveal promising successes and future challenges for RosettaDock
-
Daily M.D., Masica D., Sivasubramanian A., Somarouthu S., and Gray J.J. CAPRI rounds 3-5 reveal promising successes and future challenges for RosettaDock. Proteins 60 (2005) 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
-
36
-
-
0036468396
-
Protein-protein association kinetics and protein docking
-
Camacho C.J., and Vajda S. Protein-protein association kinetics and protein docking. Curr. Opin. Struct. Biol. 12 (2002) 36-40
-
(2002)
Curr. Opin. Struct. Biol.
, vol.12
, pp. 36-40
-
-
Camacho, C.J.1
Vajda, S.2
-
37
-
-
14644438345
-
Progress and challenges in high-resolution refinement of protein structure models
-
Misura K.M., and Baker D. Progress and challenges in high-resolution refinement of protein structure models. Proteins 59 (2005) 15-29
-
(2005)
Proteins
, vol.59
, pp. 15-29
-
-
Misura, K.M.1
Baker, D.2
-
38
-
-
24944493938
-
Toward high-resolution de novo structure prediction for small proteins
-
Bradley P., Misura K.M., and Baker D. Toward high-resolution de novo structure prediction for small proteins. Science 309 (2005) 1868-1871
-
(2005)
Science
, vol.309
, pp. 1868-1871
-
-
Bradley, P.1
Misura, K.M.2
Baker, D.3
-
39
-
-
17744364070
-
Improved side-chain modeling for protein-protein docking
-
Wang C., Schueler-Furman O., and Baker D. Improved side-chain modeling for protein-protein docking. Protein Sci. 14 (2005) 1328-1339
-
(2005)
Protein Sci.
, vol.14
, pp. 1328-1339
-
-
Wang, C.1
Schueler-Furman, O.2
Baker, D.3
-
40
-
-
0033954256
-
The Protein Data Bank
-
Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., et al. The Protein Data Bank. Nucleic Acids Res. 28 (2000) 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
-
41
-
-
0029646114
-
Crystal structure of an acetylcholinesterase-fasciculin complex: interaction of a three-fingered toxin from snake venom with its target
-
Harel M., Kleywegt G.J., Ravelli R.B., Silman I., and Sussman J.L. Crystal structure of an acetylcholinesterase-fasciculin complex: interaction of a three-fingered toxin from snake venom with its target. Structure 3 (1995) 1355-1366
-
(1995)
Structure
, vol.3
, pp. 1355-1366
-
-
Harel, M.1
Kleywegt, G.J.2
Ravelli, R.B.3
Silman, I.4
Sussman, J.L.5
-
42
-
-
0030043411
-
Structure of fasciculin 2 from green mamba snake venom: evidence for unusual loop flexibility
-
le Du M.H., Housset D., Marchot P., Bougis P.E., Navaza J., and Fontecilla-Camps J.C. Structure of fasciculin 2 from green mamba snake venom: evidence for unusual loop flexibility. Acta Crystallogr. Sect. D 52 (1996) 87-92
-
(1996)
Acta Crystallogr. Sect. D
, vol.52
, pp. 87-92
-
-
le Du, M.H.1
Housset, D.2
Marchot, P.3
Bougis, P.E.4
Navaza, J.5
Fontecilla-Camps, J.C.6
-
43
-
-
0029091444
-
Structure and internal dynamics of the bovine pancreatic trypsin inhibitor in aqueous solution from long-time molecular dynamics simulations
-
Brunne R.M., Berndt K.D., Guntert P., Wuthrich K., and van Gunsteren W.F. Structure and internal dynamics of the bovine pancreatic trypsin inhibitor in aqueous solution from long-time molecular dynamics simulations. Proteins 23 (1995) 49-62
-
(1995)
Proteins
, vol.23
, pp. 49-62
-
-
Brunne, R.M.1
Berndt, K.D.2
Guntert, P.3
Wuthrich, K.4
van Gunsteren, W.F.5
-
44
-
-
0035830963
-
Protein-protein association: investigation of factors influencing association rates by Brownian dynamics simulations
-
Gabdoulline R.R., and Wade R.C. Protein-protein association: investigation of factors influencing association rates by Brownian dynamics simulations. J. Mol. Biol. 306 (2001) 1139-1155
-
(2001)
J. Mol. Biol.
, vol.306
, pp. 1139-1155
-
-
Gabdoulline, R.R.1
Wade, R.C.2
-
45
-
-
33750337737
-
Protein complex formation by acetylcholinesterase and the neurotoxin fasciculin-2 appears to involve an induced-fit mechanism
-
Bui J.M., and McCammon J.A. Protein complex formation by acetylcholinesterase and the neurotoxin fasciculin-2 appears to involve an induced-fit mechanism. Proc. Natl Acad. Sci. USA 103 (2006) 15451-15456
-
(2006)
Proc. Natl Acad. Sci. USA
, vol.103
, pp. 15451-15456
-
-
Bui, J.M.1
McCammon, J.A.2
-
46
-
-
0031405879
-
Picosecond to hour time scale dynamics of a "three finger" toxin: correlation with its toxic and antigenic properties
-
Guenneugues M., Drevet P., Pinkasfeld S., Gilquin B., Menez A., and Zinn-Justin S. Picosecond to hour time scale dynamics of a "three finger" toxin: correlation with its toxic and antigenic properties. Biochemistry 36 (1997) 16097-16108
-
(1997)
Biochemistry
, vol.36
, pp. 16097-16108
-
-
Guenneugues, M.1
Drevet, P.2
Pinkasfeld, S.3
Gilquin, B.4
Menez, A.5
Zinn-Justin, S.6
-
47
-
-
35548976322
-
Open-to-closed transition in apo maltose-binding protein observed by paramagnetic NMR
-
Tang C., Schwieters C.D., and Clore G.M. Open-to-closed transition in apo maltose-binding protein observed by paramagnetic NMR. Nature 449 (2007) 1078-1082
-
(2007)
Nature
, vol.449
, pp. 1078-1082
-
-
Tang, C.1
Schwieters, C.D.2
Clore, G.M.3
-
48
-
-
21644480883
-
Protein-Protein Docking Benchmark 2.0: an update
-
Mintseris J., Wiehe K., Pierce B., Anderson R., Chen R., Janin J., and Weng Z. Protein-Protein Docking Benchmark 2.0: an update. Proteins 60 (2005) 214-216
-
(2005)
Proteins
, vol.60
, pp. 214-216
-
-
Mintseris, J.1
Wiehe, K.2
Pierce, B.3
Anderson, R.4
Chen, R.5
Janin, J.6
Weng, Z.7
-
49
-
-
35448929112
-
A large data set comparison of protein structures determined by crystallography and NMR: statistical test for structural differences and the effect of crystal packing
-
Andrec M., Snyder D.A., Zhou Z., Young J., Montelione G.T., and Levy R.M. A large data set comparison of protein structures determined by crystallography and NMR: statistical test for structural differences and the effect of crystal packing. Proteins 69 (2007) 449-465
-
(2007)
Proteins
, vol.69
, pp. 449-465
-
-
Andrec, M.1
Snyder, D.A.2
Zhou, Z.3
Young, J.4
Montelione, G.T.5
Levy, R.M.6
-
50
-
-
0030931612
-
Prediction of protein conformational freedom from distance constraints
-
de Groot B.L., van Aalten D.M., Scheek R.M., Amadei A., Vriend G., and Berendsen H.J. Prediction of protein conformational freedom from distance constraints. Proteins 29 (1997) 240-251
-
(1997)
Proteins
, vol.29
, pp. 240-251
-
-
de Groot, B.L.1
van Aalten, D.M.2
Scheek, R.M.3
Amadei, A.4
Vriend, G.5
Berendsen, H.J.6
-
51
-
-
34249945151
-
Insights into equilibrium dynamics of proteins from comparison of NMR and X-ray data with computational predictions
-
Yang L.W., Eyal E., Chennubhotla C., Jee J., Gronenborn A.M., and Bahar I. Insights into equilibrium dynamics of proteins from comparison of NMR and X-ray data with computational predictions. Structure 15 (2007) 741-749
-
(2007)
Structure
, vol.15
, pp. 741-749
-
-
Yang, L.W.1
Eyal, E.2
Chennubhotla, C.3
Jee, J.4
Gronenborn, A.M.5
Bahar, I.6
-
52
-
-
48449086707
-
-
Sivasubramanian, A., Sircar, A., Chaudhury, S. & Gray, J. J. (2008). Towards high-resolution homology modeling of antibody Fv regions using knowledge-based techniques, de novo loop modeling and docking. Manuscript in preparation.
-
Sivasubramanian, A., Sircar, A., Chaudhury, S. & Gray, J. J. (2008). Towards high-resolution homology modeling of antibody Fv regions using knowledge-based techniques, de novo loop modeling and docking. Manuscript in preparation.
-
-
-
-
53
-
-
36749091035
-
Assessing the energy landscape of CAPRI targets by FunHunt
-
London N., and Schueler-Furman O. Assessing the energy landscape of CAPRI targets by FunHunt. Proteins 69 (2007) 809-815
-
(2007)
Proteins
, vol.69
, pp. 809-815
-
-
London, N.1
Schueler-Furman, O.2
-
54
-
-
21644473891
-
Representing receptor flexibility in ligand docking through relevant normal modes
-
Cavasotto C.N., Kovacs J.A., and Abagyan R.A. Representing receptor flexibility in ligand docking through relevant normal modes. J. Am. Chem. Soc. 127 (2005) 9632-9640
-
(2005)
J. Am. Chem. Soc.
, vol.127
, pp. 9632-9640
-
-
Cavasotto, C.N.1
Kovacs, J.A.2
Abagyan, R.A.3
-
55
-
-
34247500337
-
Exploring multiple timescale motions in protein GB3 using accelerated molecular dynamics and NMR spectroscopy
-
Markwick P.R., Bouvignies G., and Blackledge M. Exploring multiple timescale motions in protein GB3 using accelerated molecular dynamics and NMR spectroscopy. J. Am. Chem. Soc. 129 (2007) 4724-4730
-
(2007)
J. Am. Chem. Soc.
, vol.129
, pp. 4724-4730
-
-
Markwick, P.R.1
Bouvignies, G.2
Blackledge, M.3
-
56
-
-
35748982413
-
Geometry-based sampling of conformational transitions in proteins
-
Seeliger D., Haas J., and de Groot B.L. Geometry-based sampling of conformational transitions in proteins. Structure 15 (2007) 1482-1492
-
(2007)
Structure
, vol.15
, pp. 1482-1492
-
-
Seeliger, D.1
Haas, J.2
de Groot, B.L.3
-
57
-
-
21644483402
-
Docking to single-domain and multiple-domain proteins: old and new challenges
-
Ben-Zeev E., Kowalsman N., Ben-Shimon A., Segal D., Atarot T., Noivirt O., et al. Docking to single-domain and multiple-domain proteins: old and new challenges. Proteins 60 (2005) 195-201
-
(2005)
Proteins
, vol.60
, pp. 195-201
-
-
Ben-Zeev, E.1
Kowalsman, N.2
Ben-Shimon, A.3
Segal, D.4
Atarot, T.5
Noivirt, O.6
-
59
-
-
30044434744
-
Structural changes involved in protein binding correlate with intrinsic motions of proteins in the unbound state
-
Tobi D., and Bahar I. Structural changes involved in protein binding correlate with intrinsic motions of proteins in the unbound state. Proc. Natl Acad. Sci. USA. 102 (2005) 18908-18913
-
(2005)
Proc. Natl Acad. Sci. USA.
, vol.102
, pp. 18908-18913
-
-
Tobi, D.1
Bahar, I.2
-
60
-
-
34447558566
-
Constructing ensembles of flexible fragments in native proteins by iterative stochastic elimination is relevant to protein-protein interfaces
-
Noy E., Tabakman T., and Goldblum A. Constructing ensembles of flexible fragments in native proteins by iterative stochastic elimination is relevant to protein-protein interfaces. Proteins 68 (2007) 702-711
-
(2007)
Proteins
, vol.68
, pp. 702-711
-
-
Noy, E.1
Tabakman, T.2
Goldblum, A.3
-
61
-
-
36749098356
-
The performance of ZDOCK and ZRANK in rounds 6-11 of CAPRI
-
Wiehe K., Pierce B., Tong W.W., Hwang H., Mintseris J., and Weng Z. The performance of ZDOCK and ZRANK in rounds 6-11 of CAPRI. Proteins 69 (2007) 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
Weng, Z.6
-
63
-
-
0038021436
-
Assessment of blind predictions of protein-protein interactions: current status of docking methods
-
Mendez R., Leplae R., De Maria L., and Wodak S.J. 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
-
-
Mendez, R.1
Leplae, R.2
De Maria, L.3
Wodak, S.J.4
-
64
-
-
33644839662
-
Structural model of the mAb 806-EGFR complex using computational docking followed by computational and experimental mutagenesis
-
Sivasubramanian A., Chao G., Pressler H.M., Wittrup K.D., and Gray J.J. Structural model of the mAb 806-EGFR complex using computational docking followed by computational and experimental mutagenesis. Structure 14 (2006) 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
-
65
-
-
37349109629
-
Modeling the structure of mAb 14B8 bound to the anthrax protective antigen
-
Sivasubramanian A., Maynard J.A., and Gray J.J. Modeling the structure of mAb 14B8 bound to the anthrax protective antigen. Proteins 70 (2008) 218-230
-
(2008)
Proteins
, vol.70
, pp. 218-230
-
-
Sivasubramanian, A.1
Maynard, J.A.2
Gray, J.J.3
-
66
-
-
0031585984
-
Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions
-
Simons K.T., Kooperberg C., Huang E., and Baker D. Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. J. Mol. Biol. 268 (1997) 209-225
-
(1997)
J. Mol. Biol.
, vol.268
, pp. 209-225
-
-
Simons, K.T.1
Kooperberg, C.2
Huang, E.3
Baker, D.4
|