-
2
-
-
0033970020
-
Folding and binding cascades: Dynamic landscapes and population shifts
-
Kumar S, Ma B, Tsai CJ, Sinha N, Nussinov R. Folding and binding cascades: dynamic landscapes and population shifts. Protein Sci 2000; 9: 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
-
3
-
-
0035451185
-
Structured disorder and conformational selection
-
Tsai CJ, Ma B, Sham YY, Kumar S, Nussinov R. Structured disorder and conformational selection. Proteins 2001; 44: 418-427.
-
(2001)
Proteins
, vol.44
, pp. 418-427
-
-
Tsai, C.J.1
Ma, B.2
Sham, Y.Y.3
Kumar, S.4
Nussinov, R.5
-
4
-
-
0037470496
-
Antibody multispecificity mediated by conformational diversity
-
James LC, Roversi P, Tawfik DS. Antibody multispecificity mediated by conformational diversity. Science 2003; 299: 1362-1367.
-
(2003)
Science
, vol.299
, pp. 1362-1367
-
-
James, L.C.1
Roversi, P.2
Tawfik, D.S.3
-
5
-
-
0036147568
-
Multiple diverse ligands binding at a single protein site: A matter of pre-existing populations
-
Ma B, Shatsky M, Wolfson HJ, Nussinov R. Multiple diverse ligands binding at a single protein site: a matter of pre-existing populations. Protein Sci 2002; 11: 184-197.
-
(2002)
Protein Sci
, vol.11
, pp. 184-197
-
-
Ma, B.1
Shatsky, M.2
Wolfson, H.J.3
Nussinov, R.4
-
6
-
-
0001858251
-
Application of a theory of enzyme specificity to protein synthesis
-
Koshland DE. Application of a theory of enzyme specificity to protein synthesis. Proc Natl Acad Sci USA 1958; 44: 98-104.
-
(1958)
Proc Natl Acad Sci USA
, vol.44
, pp. 98-104
-
-
Koshland, D.E.1
-
7
-
-
1342302339
-
Conformational changes associated with protein-protein interactions
-
Goh CS, Milburn D, Gerstein M, Conformational changes associated with protein-protein interactions. Curr Opin Chem Biol 2004; 14: 1-6.
-
(2004)
Curr Opin Chem Biol
, vol.14
, pp. 1-6
-
-
Goh, C.S.1
Milburn, D.2
Gerstein, M.3
-
8
-
-
9944237833
-
Complementarity of structure ensembles in protein-protein binding
-
Grunberg R, Leckner J, Nilges M. Complementarity of structure ensembles in protein-protein binding. Struct 2004; 12: 2125-2136.
-
(2004)
Struct
, vol.12
, pp. 2125-2136
-
-
Grunberg, R.1
Leckner, J.2
Nilges, M.3
-
9
-
-
70350340728
-
The role of dynamic conformational ensembles in biomolecular recognition
-
Boehr DD, Nussinov R, Wright PE. The role of dynamic conformational ensembles in biomolecular recognition. Nat Chem Biol 2009; 5: 789-796.
-
(2009)
Nat Chem Biol
, vol.5
, pp. 789-796
-
-
Boehr, D.D.1
Nussinov, R.2
Wright, P.E.3
-
11
-
-
15244355250
-
The relationship between the flexibility of proteins and their conformational states on forming protein-protein complexes with application to protein-protein docking
-
Smith GR, Sternberg MJE, Bates PA. The relationship between the flexibility of proteins and their conformational states on forming protein-protein complexes with application to protein-protein docking. J mol Biol 2005; 347: 1077-1101.
-
(2005)
J Mol Biol
, vol.347
, pp. 1077-1101
-
-
Smith, G.R.1
Sternberg, M.J.E.2
Bates, P.A.3
-
12
-
-
21644460933
-
Docking essential dynamics eigenstructures
-
Mustard D, Ritchie DH. Docking essential dynamics eigenstructures. Proteins 2005; 60: 269-274.
-
(2005)
Proteins
, vol.60
, pp. 269-274
-
-
Mustard, D.1
Ritchie, D.H.2
-
13
-
-
36749057349
-
Implicit flexibility in protein docking: Cross-docking and local refinement
-
Król M, Chaleil RA, Tournier AL, Bates PA. Implicit flexibility in protein docking: cross-docking and local refinement. Proteins 2007; 69: 750-757.
-
(2007)
Proteins
, vol.69
, pp. 750-757
-
-
Król, M.1
Chaleil, R.A.2
Tournier, A.L.3
Bates, P.A.4
-
14
-
-
48449094112
-
Conformer selection and induced fit in flexible backbone protein-protein docking using computational and NMR ensembles
-
Chaudhury S, Gray JJ. Conformer selection and induced fit in flexible backbone protein-protein docking using computational and NMR ensembles. J Mol Biol 2008; 381: 1068-1087.
-
(2008)
J Mol Biol
, vol.381
, pp. 1068-1087
-
-
Chaudhury, S.1
Gray, J.J.2
-
16
-
-
33644843079
-
Accounting for loop flexibility during protein-protein docking
-
Bastard K, Prevost C, Zacharias M. Accounting for loop flexibility during protein-protein docking. Proteins 2006; 62: 956-969.
-
(2006)
Proteins
, vol.62
, pp. 956-969
-
-
Bastard, K.1
Prevost, C.2
Zacharias, M.3
-
17
-
-
0037442962
-
HADDOCK: A protein-protein docking approach based on biochemical or biophysical information
-
Dominguez C, Boelens R, Bonvin A. HADDOCK: a protein-protein docking approach based on biochemical or biophysical information. J Amer Chem. Soc 2003; 125: 1731-1737.
-
(2003)
J Amer Chem. Soc
, vol.125
, pp. 1731-1737
-
-
Dominguez, C.1
Boelens, R.2
Bonvin, A.3
-
18
-
-
0038697837
-
Guided docking: First step to locate potential binding sites
-
Fitzjohn PW, Bates PA. Guided docking: first step to locate potential binding sites. Proteins 2003; 52: 28-32.
-
(2003)
Proteins
, vol.52
, pp. 28-32
-
-
Fitzjohn, P.W.1
Bates, P.A.2
-
19
-
-
21644477228
-
Incorporation of flexibility into rigid-body docking: Applications in rounds 3-5 of CAPRI
-
Smith GR, Fitzjohn PW, Page CS, Bates PA. Incorporation of flexibility into rigid-body docking: applications in rounds 3-5 of CAPRI. Proteins 2005; 60: 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
-
20
-
-
34249884544
-
Flexible relaxation of rigid-body docking solutions
-
Krol M, Tournier AL, Bates PA. Flexible relaxation of rigid-body docking solutions. Proteins 2007; 68: 159-169.
-
(2007)
Proteins
, vol.68
, pp. 159-169
-
-
Krol, M.1
Tournier, A.L.2
Bates, P.A.3
-
21
-
-
36748998784
-
HADDOCK versus HADDOCK: New features and performance of HADDOCK2.0 on the CAPRI targets
-
de Vries SJ, van Dijk AD, Krzeminski M, van Dijk M, Thureau A, Hsu V, Wassenaar T, Bonvin AM. HADDOCK versus HADDOCK: new features and performance of HADDOCK2.0 on the CAPRI targets. Proteins 2007; 69: 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
Wassenaar, T.7
Bonvin, A.M.8
-
22
-
-
34548861782
-
Protein-protein docking with backbone flexibility
-
Wang C, Bradley P, Baker D. Protein-protein docking with backbone flexibility. J Mol Biol 2007; 373: 505-515.
-
(2007)
J Mol Biol
, vol.373
, pp. 505-515
-
-
Wang, C.1
Bradley, P.2
Baker, D.3
-
23
-
-
36749075510
-
Incorporating biochemical information and backbone flexibility in RosettaDock for CAPRI rounds 6-12
-
Chaudhury S, Sircar A, Sivasubramanian A, Berrando M, Gray JJ. Incorporating biochemical information and backbone flexibility in RosettaDock for CAPRI rounds 6-12. Proteins 2007; 69: 793-800.
-
(2007)
Proteins
, vol.69
, pp. 793-800
-
-
Chaudhury, S.1
Sircar, A.2
Sivasubramanian, A.3
Berrando, M.4
Gray, J.J.5
-
24
-
-
23344454719
-
Refinement of docked protein-ligand and protein-DNA structures using low frequency normal mode amplitude optimization
-
Lindahl E, Delarue M. Refinement of docked protein-ligand and protein-DNA structures using low frequency normal mode amplitude optimization. Nucleic Acids Res 2005; 33: 4496-4506.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 4496-4506
-
-
Lindahl, E.1
Delarue, M.2
-
25
-
-
38549097715
-
Energy minimization in low-frequency normal modes to efficiently allow for global flexibility during systematic protein-protein docking
-
May A, Zacharias M. Energy minimization in low-frequency normal modes to efficiently allow for global flexibility during systematic protein-protein docking. Proteins 2008; 70: 794-809.
-
(2008)
Proteins
, vol.70
, pp. 794-809
-
-
May, A.1
Zacharias, M.2
-
26
-
-
0000197372
-
Large amplitude elastic motions in proteins from a single-parameter, atomic analysis
-
Tirion MM. Large amplitude elastic motions in proteins from a single-parameter, atomic analysis. Phys Rev Lett 1996; 77: 1905-1908.
-
(1996)
Phys Rev Lett
, vol.77
, pp. 1905-1908
-
-
Tirion, M.M.1
-
27
-
-
0032533790
-
Analysis of domain motions by approximate normal mode calculations
-
Hinsen K. Analysis of domain motions by approximate normal mode calculations. Proteins 1998; 33: 417-429.
-
(1998)
Proteins
, vol.33
, pp. 417-429
-
-
Hinsen, K.1
-
28
-
-
1642365068
-
New advances in normal mode analysis of supermolecular complexes and applications to structural refinement
-
Ma J. New advances in normal mode analysis of supermolecular complexes and applications to structural refinement. Curr Protein Pept Sci 2004; 5: 119-123.
-
(2004)
Curr Protein Pept Sci
, vol.5
, pp. 119-123
-
-
Ma, J.1
-
29
-
-
0035044995
-
Conformational change of proteins arising from normal mode calculations
-
Tama F, Sanejouand YH. Conformational change of proteins arising from normal mode calculations. Protein Eng 2001; 14: 1-6.
-
(2001)
Protein Eng
, vol.14
, pp. 1-6
-
-
Tama, F.1
Sanejouand, Y.H.2
-
30
-
-
29144485503
-
Accounting for global protein deformability during protein-protein and protein-ligand docking
-
May A, Zacharias M. Accounting for global protein deformability during protein-protein and protein-ligand docking. Biochim Biophys Acta 2005; 1754: 225-231.
-
(2005)
Biochim Biophys Acta
, vol.1754
, pp. 225-231
-
-
May, A.1
Zacharias, M.2
-
31
-
-
33646145523
-
Can conformational change be described by only a few normal modes?
-
Petrone P, Pande VS. Can conformational change be described by only a few normal modes? Biophys J 2006; 90: 1583-1593.
-
(2006)
Biophys J
, vol.90
, pp. 1583-1593
-
-
Petrone, P.1
Pande, V.S.2
-
32
-
-
48749126860
-
Insights into protein flexibility: The relationship between normal modes and conformational change upon protein-protein docking
-
Dobbins SE, Lesk VI, Sternberg MJ. Insights into protein flexibility: the relationship between normal modes and conformational change upon protein-protein docking. Proc Natl Acad Sci USA 2008; 105: 10390-10395.
-
(2008)
Proc Natl Acad Sci USA
, vol.105
, pp. 10390-10395
-
-
Dobbins, S.E.1
Lesk, V.I.2
Sternberg, M.J.3
-
33
-
-
21644473891
-
Representing receptor flexibility in ligand docking through relevant normal modes
-
Cavasotto CN, Kovacs JA, Abagyan RA. Representing receptor flexibility in ligand docking through relevant normal modes. J Am Chem Soc 2005; 127: 9632-9640.
-
(2005)
J Am Chem Soc
, vol.127
, pp. 9632-9640
-
-
Cavasotto, C.N.1
Kovacs, J.A.2
Abagyan, R.A.3
-
34
-
-
34548317146
-
FireDock: Fast interaction refinement in molecular docking
-
Andrusier N, Nussinov R, Wolfson HJ. FireDock: fast interaction refinement in molecular docking. Proteins 2007; 69: 139-159.
-
(2007)
Proteins
, vol.69
, pp. 139-159
-
-
Andrusier, N.1
Nussinov, R.2
Wolfson, H.J.3
-
35
-
-
0038161052
-
Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations
-
Gray JJ, Moughon S, Schueler-Furman. O, Kuhlman B, Rohi 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
Schueler-Furman, O.3
Kuhlman, B.4
Rohi, C.A.5
Baker, D.6
-
36
-
-
68549106477
-
Side chain-positioning as an integer programming problem
-
Eriksson O. Side chain-positioning as an integer programming problem. Lect Notes in Comput Sci 2001; 2149: 128-141.
-
(2001)
Lect Notes in Comput Sci
, vol.2149
, pp. 128-141
-
-
Eriksson, O.1
-
37
-
-
77958398767
-
The convergence of a class of double-rank minimization algorithms
-
Broyden CG. The convergence of a class of double-rank minimization algorithms. J Inst Math Appl 1970; 6: 76-90.
-
(1970)
J Inst Math Appl
, vol.6
, pp. 76-90
-
-
Broyden, C.G.1
-
38
-
-
0014825610
-
A new approach to variable metric algorithms
-
Fletcher R. A new approach to variable metric algorithms. Comput J 1970; 13: 317-322.
-
(1970)
Comput J
, vol.13
, pp. 317-322
-
-
Fletcher, R.1
-
39
-
-
0035132230
-
Anisotropy of fluctuation dynamics of proteins with an elastic network model
-
Atilgan AR, Durell SR, Jernigan RL, Demirel MC, Keskin O, Bahar I. Anisotropy of fluctuation dynamics of proteins with an elastic network model. Biophys J 2001; 80: 505-515.
-
(2001)
Biophys J
, vol.80
, pp. 505-515
-
-
Atilgan, A.R.1
Durell, S.R.2
Jernigan, R.L.3
Demirel, M.C.4
Keskin, O.5
Bahar, I.6
-
40
-
-
0041784950
-
All-atom empirical potential for molecular modeling and dynamics studies of proteins
-
MacKerell AD Jr, Bashford D, Bellott M, Dunbrack RL Jr, Evanseck JD, Field MJ, Fischer S, Gao J, Guo H, Ha S, Joseph-McCarthy D, Kuchnir L, Kuczera K, Lau FTK, Mattos C, Michnick S, Ngo T, Nguyen DT, Prodhom B, Reiher WE III, Roux B, Schlenkrich M, Smith JC, Stote R, Straub J, Watanabe M, Wiórkiewicz-Kuczera J, Yin D, Karplus M. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem 1998; 102: 3586-3616.
-
(1998)
J Phys Chem
, vol.102
, pp. 3586-3616
-
-
Jr, M.A.D.1
Bashford, D.2
Bellott, M.3
Jr, D.R.L.4
Evanseck, J.D.5
Field, M.J.6
Fischer, S.7
Gao, J.8
Guo, H.9
Ha, S.10
Joseph-McCarthy, D.11
Kuchnir, L.12
Kuczera, K.13
Lau, F.T.K.14
Mattos, C.15
Michnick, S.16
Ngo, T.17
Nguyen, D.T.18
Prodhom, B.19
Iii, R.W.E.20
Roux, B.21
Schlenkrich, M.22
Smith, J.C.23
Stote, R.24
Straub, J.25
Watanabe, M.26
Wiórkiewicz- Kuczera, J.27
Yin, D.28
Karplus, M.29
more..
-
41
-
-
0037406075
-
Cyclic coordinate descent: A robotics algorithm for protein loop closure
-
Dunbrack RL Jr, Canutescu AA. Cyclic coordinate descent: a robotics algorithm for protein loop closure. Protein Sci 2003; 12: 963-972.
-
(2003)
Protein Sci
, vol.12
, pp. 963-972
-
-
Jr, D.R.L.1
Canutescu, A.A.2
-
42
-
-
0038021436
-
Assessment of blind predictions of protein-protein interactions: Current status of docking methods
-
Mendez. R, Leplae R, De Maria L, Wodak. SJ. Assessment of blind predictions of protein-protein interactions: current status of docking methods. Proteins 2003; 52: 51-67.
-
(2003)
Proteins
, vol.52
, pp. 51-67
-
-
Mendez, R.1
Leplae, R.2
De Maria, L.3
Wodak, S.J.4
-
43
-
-
84956979675
-
Efficient unbound docking of rigid molecules
-
Guigo R, Gusfieid D, editors. Italy, Springer Verlag
-
Duhovny D, Nussinov R, Wolfson HJ. Efficient unbound docking of rigid molecules. In: Guigo R, Gusfieid D, editors. Proceedings of the 2'nd Workshop on Algorithms in Bioinformatics (WABI) Rome, Italy, Vol.2452, Springer Verlag; 2002. pp 185-200.
-
(2002)
Proceedings of the 2'nd Workshop on Algorithms in Bioinformatics (WABI) Rome
, vol.2452
, pp. 185-200
-
-
Duhovny, D.1
Nussinov, R.2
Wolfson, H.J.3
-
45
-
-
36749006579
-
Docking and scoring protein complexes: CAPRI 3rd edition
-
Lensink MF, Wodak SJ, Mendez R. Docking and scoring protein complexes: CAPRI 3rd edition. Proteins 2007; 69: 704-718.
-
(2007)
Proteins
, vol.69
, pp. 704-718
-
-
Lensink, M.F.1
Wodak, S.J.2
Mendez, R.3
-
46
-
-
21644469377
-
Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures
-
Mendez R, Leplae R, Lensink MF, Wodak SJ. Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures. Proteins 2005; 60: 150-169.
-
(2005)
Proteins
, vol.60
, pp. 150-169
-
-
Mendez, R.1
Leplae, R.2
Lensink, M.F.3
Wodak, S.J.4
-
47
-
-
0038237369
-
Taking geometry to its edge: Fast unbound rigid (and hingebent) docking
-
Schneidman-Duhovny D, Inbar Y, Polak V, Shatsky M, Halperin I, Benyamini H, Barzilai A, Dror O, Haspel N, Nussinov R, Wolfson HJ. Taking geometry to its edge: fast unbound rigid (and hingebent) docking. Proteins 2003; 52: 107-112.
-
(2003)
Proteins
, vol.52
, pp. 107-112
-
-
Schneidman-Duhovny, D.1
Inbar, Y.2
Polak, V.3
Shatsky, M.4
Halperin, I.5
Benyamini, H.6
Barzilai, A.7
Dror, O.8
Haspel, N.9
Nussinov, R.10
Wolfson, H.J.11
-
48
-
-
4444221565
-
UCSF Chimera -a visualization system for exploratory research and analysis
-
Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE. UCSF Chimera -a visualization system for exploratory research and analysis. J Comput Chem 2004; 25: 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
-
49
-
-
34447286908
-
The third CAPRI assessment meeting, Toronto, Canada, April 20-2.1
-
Janin J, Wodak S. The third CAPRI assessment meeting, Toronto, Canada, April 20-2.1, 2007. Structure 2007; 15: 755-759.
-
(2007)
Structure
, vol.2007
, Issue.15
, pp. 755-759
-
-
Janin, J.1
Wodak, S.2
-
50
-
-
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
-
51
-
-
27344449197
-
Progress in modeling of protein structures and interactions
-
Schueler-Furman O, Wang C, Bradley P, Misura K, Baker D. Progress in modeling of protein structures and interactions. Science 2005; 310: 638-642.
-
(2005)
Science
, vol.310
, pp. 638-642
-
-
Schueler-Furman, O.1
Wang, C.2
Bradley, P.3
Misura, K.4
Baker, D.5
-
52
-
-
39749202824
-
HingeProt: Automated prediction of hinges in protein structures
-
Emekli U, Schneidman-Duhovny D, Wolfson HJ, Nussinov R, Haliloglu T. HingeProt: automated prediction of hinges in protein structures. Proteins 2008; 70: 1219-1227.
-
(2008)
Proteins
, vol.70
, pp. 1219-1227
-
-
Emekli, U.1
Schneidman-Duhovny, D.2
Wolfson, H.J.3
Nussinov, R.4
Haliloglu, T.5
-
53
-
-
36749077465
-
Automatic prediction of protein interactions with large scale motion
-
Schneidman-Duhovny D, Nussinov R, Wolfson HJ. Automatic prediction of protein interactions with large scale motion. Proteins 2007; 69: 764-773.
-
(2007)
Proteins
, vol.69
, pp. 764-773
-
-
Schneidman-Duhovny, D.1
Nussinov, R.2
Wolfson, H.J.3
|