-
1
-
-
0034978909
-
Correlated conformational fluctuations during enzymatic catalysis: Implications for catalytic rate enhancement
-
Alper KO, Singla M, Stone JL, Bagdassarian CK. Correlated conformational fluctuations during enzymatic catalysis: implications for catalytic rate enhancement. Protein Sci 2001;10:1319-1330.
-
(2001)
Protein Sci
, vol.10
, pp. 1319-1330
-
-
Alper, K.O.1
Singla, M.2
Stone, J.L.3
Bagdassarian, C.K.4
-
2
-
-
27744499156
-
Intrinsic dynamics of an enzyme underlies catalysis
-
Eisenmesser EZ, Millet O, Labeikovsky W, Korzhnev DM, Wolf-Watz M, Bosco DA, Skalicky JJ, Kay LE, Kern D. Intrinsic dynamics of an enzyme underlies catalysis. Nature 2005;438:117-121.
-
(2005)
Nature
, vol.438
, pp. 117-121
-
-
Eisenmesser, E.Z.1
Millet, O.2
Labeikovsky, W.3
Korzhnev, D.M.4
Wolf-Watz, M.5
Bosco, D.A.6
Skalicky, J.J.7
Kay, L.E.8
Kern, D.9
-
3
-
-
31944448999
-
Coupling of structural fluctuations to deamidation reaction in triosephosphate isomerase by Gaussian network model
-
Konuklar FA, Aviyente V, Haliloglu T. Coupling of structural fluctuations to deamidation reaction in triosephosphate isomerase by Gaussian network model. Proteins 2006;62:715-727.
-
(2006)
Proteins
, vol.62
, pp. 715-727
-
-
Konuklar, F.A.1
Aviyente, V.2
Haliloglu, T.3
-
4
-
-
22044451713
-
Coupled motions in the SH2 and kinase domains of Csk control Src phosphorylation
-
Wong L, Lieser SA, Miyashita O, Miller M, Tasken K, Onuchic JN, Adams JA, Woods VL, Jr., Jennings PA. Coupled motions in the SH2 and kinase domains of Csk control Src phosphorylation. J Mol Biol 2005;351:131-143.
-
(2005)
J Mol Biol
, vol.351
, pp. 131-143
-
-
Wong, L.1
Lieser, S.A.2
Miyashita, O.3
Miller, M.4
Tasken, K.5
Onuchic, J.N.6
Adams, J.A.7
Woods Jr., V.L.8
Jennings, P.A.9
-
5
-
-
20444409186
-
Coupling between catalytic site and collective dynamics: A requirement for mechanochemical activity of enzymes
-
Yang LW, Bahar I. Coupling between catalytic site and collective dynamics: a requirement for mechanochemical activity of enzymes. Structure 2005;13:893-904.
-
(2005)
Structure
, vol.13
, pp. 893-904
-
-
Yang, L.W.1
Bahar, I.2
-
6
-
-
23244458844
-
Specificity of trypsin and chymotrypsin: Loop-motion-controlled dynamic correlation as a determinant
-
Ma W, Tang C, Lai L. Specificity of trypsin and chymotrypsin: loop-motion-controlled dynamic correlation as a determinant. Biophys J 2005;89:1183-1193.
-
(2005)
Biophys J
, vol.89
, pp. 1183-1193
-
-
Ma, W.1
Tang, C.2
Lai, L.3
-
7
-
-
0033548074
-
Enzyme specificity under dynamic control: A normal mode analysis of α-lytic protease
-
Miller DW, Agard DA. Enzyme specificity under dynamic control: a normal mode analysis of α-lytic protease. J Mol Biol 1999;286:267-278.
-
(1999)
J Mol Biol
, vol.286
, pp. 267-278
-
-
Miller, D.W.1
Agard, D.A.2
-
8
-
-
0034966704
-
Enzyme specificity under dynamic control. II: Principal component analysis of α-lytic protease using global and local solvent boundary conditions
-
Ota N, Agard DA. Enzyme specificity under dynamic control. II: Principal component analysis of α-lytic protease using global and local solvent boundary conditions. Protein Sci 2001;10:1403-1414.
-
(2001)
Protein Sci
, vol.10
, pp. 1403-1414
-
-
Ota, N.1
Agard, D.A.2
-
10
-
-
0035937443
-
Two-state allosteric behavior in a single-domain signaling protein
-
Volkman BF, Lipson D, Wemmer DE, Kern D. Two-state allosteric behavior in a single-domain signaling protein. Science 2001;291:2429-2433.
-
(2001)
Science
, vol.291
, pp. 2429-2433
-
-
Volkman, B.F.1
Lipson, D.2
Wemmer, D.E.3
Kern, D.4
-
11
-
-
0042424707
-
Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy
-
Tama F, Valle M, Frank J, Brooks CL, III. Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy. Proc Natl Acad Sci USA 2003;100:9319-9323.
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 9319-9323
-
-
Tama, F.1
Valle, M.2
Frank, J.3
Brooks III, C.L.4
-
12
-
-
4344685227
-
Global ribosome motions revealed with elastic network model
-
Wang Y, Rader AJ, Bahar I, Jernigan RL. Global ribosome motions revealed with elastic network model. J Struct Biol 2004;147:302-314.
-
(2004)
J Struct Biol
, vol.147
, pp. 302-314
-
-
Wang, Y.1
Rader, A.J.2
Bahar, I.3
Jernigan, R.L.4
-
13
-
-
0034691576
-
A ratchet-like inter-subunit reorganization of the ribosome during translocation
-
Frank J, Agrawal RK. A ratchet-like inter-subunit reorganization of the ribosome during translocation. Nature 2000;406:318-322.
-
(2000)
Nature
, vol.406
, pp. 318-322
-
-
Frank, J.1
Agrawal, R.K.2
-
14
-
-
33745714416
-
Cooperative fluctuations point to the dimerization interface of p53 core domain
-
Kantarci N, Doruker P, Haliloglu T. Cooperative fluctuations point to the dimerization interface of p53 core domain. Biophys J 2006;91:421-432.
-
(2006)
Biophys J
, vol.91
, pp. 421-432
-
-
Kantarci, N.1
Doruker, P.2
Haliloglu, T.3
-
15
-
-
33749367332
-
Association of putative concave protein-binding sites with the fluctuation behavior of residues
-
Ertekin A, Nussinov R, Haliloglu T. Association of putative concave protein-binding sites with the fluctuation behavior of residues. Protein Sci 2006;15:2265-2277.
-
(2006)
Protein Sci
, vol.15
, pp. 2265-2277
-
-
Ertekin, A.1
Nussinov, R.2
Haliloglu, T.3
-
16
-
-
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
-
17
-
-
33645961330
-
Flexible protein-protein docking
-
Bonvin AM. Flexible protein-protein docking. Curr Opin Struct Biol 2006;16:194-200.
-
(2006)
Curr Opin Struct Biol
, vol.16
, pp. 194-200
-
-
Bonvin, A.M.1
-
18
-
-
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
-
19
-
-
2942582560
-
A structural perspective on protein-protein interactions
-
Russell RB, Alber F, Aloy P, Davis FP, Korkin D, Pichaud M, Topf M, Sali A. A structural perspective on protein-protein interactions. Curr Opin Struct Biol 2004;14:313-324.
-
(2004)
Curr Opin Struct Biol
, vol.14
, pp. 313-324
-
-
Russell, R.B.1
Alber, F.2
Aloy, P.3
Davis, F.P.4
Korkin, D.5
Pichaud, M.6
Topf, M.7
Sali, A.8
-
20
-
-
1042275583
-
A dissection of specific and nonspecific protein-protein interfaces
-
Bahadur RP, Chakrabarti P, Rodier F, Janin J. A dissection of specific and nonspecific protein-protein interfaces. J Mol Biol 2004;336:943-955.
-
(2004)
J Mol Biol
, vol.336
, pp. 943-955
-
-
Bahadur, R.P.1
Chakrabarti, P.2
Rodier, F.3
Janin, J.4
-
21
-
-
33744797911
-
A combinatorial score to distinguish biological and nonbiological protein-protein interfaces. Proteins: Struct Funct
-
Liu S, Li Q, Lai L. A combinatorial score to distinguish biological and nonbiological protein-protein interfaces. Proteins: Struct Funct Bioinformatics 2006;64:68-78.
-
(2006)
Bioinformatics
, vol.64
, pp. 68-78
-
-
Liu, S.1
Li, Q.2
Lai, L.3
-
22
-
-
0035914476
-
Conservation helps to identify biologically relevant crystal contacts
-
Valdar WS, Thornton JM. Conservation helps to identify biologically relevant crystal contacts. J Mol Biol 2001;313:399-416.
-
(2001)
J Mol Biol
, vol.313
, pp. 399-416
-
-
Valdar, W.S.1
Thornton, J.M.2
-
23
-
-
0035853028
-
Identification of protein oligomerization states by analysis of interface conservation
-
Elcock AH, McCammon JA. Identification of protein oligomerization states by analysis of interface conservation. Proc Natl Acad Sci USA 2001;98:2990-2994.
-
(2001)
Proc Natl Acad Sci USA
, vol.98
, pp. 2990-2994
-
-
Elcock, A.H.1
McCammon, J.A.2
-
24
-
-
0034308172
-
Discriminating between homodimeric and monomeric proteins in the crystalline state
-
Ponstingl H, Henrick K, Thornton JM. Discriminating between homodimeric and monomeric proteins in the crystalline state. Proteins: Struct Funct Genet 2000;41:47-57.
-
(2000)
Proteins: Struct Funct Genet
, vol.41
, pp. 47-57
-
-
Ponstingl, H.1
Henrick, K.2
Thornton, J.M.3
-
25
-
-
0032169688
-
PQS: A protein quaternary structure file server
-
Henrick K, Thornton JM. PQS: a protein quaternary structure file server. Trends Biochem Sci 1998;23:358-361.
-
(1998)
Trends Biochem Sci
, vol.23
, pp. 358-361
-
-
Henrick, K.1
Thornton, J.M.2
-
27
-
-
27344440132
-
Conservation and relative importance of residues across protein-protein interfaces
-
Guharoy M, Chakrabarti P. Conservation and relative importance of residues across protein-protein interfaces. Proc Natl Acad Sci USA 2005;102:15447-15452.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 15447-15452
-
-
Guharoy, M.1
Chakrabarti, P.2
-
28
-
-
0031297461
-
Specific versus non-specific contacts in protein crystals
-
Janin J. Specific versus non-specific contacts in protein crystals. Nat Struct Biol 1997;4:973-974.
-
(1997)
Nat Struct Biol
, vol.4
, pp. 973-974
-
-
Janin, J.1
-
29
-
-
23044487169
-
Statistical analysis and prediction of protein-protein interfaces
-
Bordner AJ, Abagyan R. Statistical analysis and prediction of protein-protein interfaces. Proteins 2005;60:353-366.
-
(2005)
Proteins
, vol.60
, pp. 353-366
-
-
Bordner, A.J.1
Abagyan, R.2
-
30
-
-
0031565729
-
Analysis of protein-protein interaction sites using surface patches
-
Jones S, Thornton JM. Analysis of protein-protein interaction sites using surface patches. J Mol Biol 1997;272:121-132.
-
(1997)
J Mol Biol
, vol.272
, pp. 121-132
-
-
Jones, S.1
Thornton, J.M.2
-
31
-
-
0242299207
-
Atomic contact vectors in protein-protein recognition
-
Mintseris J, Weng Z. Atomic contact vectors in protein-protein recognition. Proteins 2003;53:629-639.
-
(2003)
Proteins
, vol.53
, pp. 629-639
-
-
Mintseris, J.1
Weng, Z.2
-
32
-
-
0141669302
-
Automatic inference of protein quaternary structure from crystals
-
Ponstingl H, Kabir T, Thornton JM. Automatic inference of protein quaternary structure from crystals. J Appl Crystallogr 2003;36:1116-1122.
-
(2003)
J Appl Crystallogr
, vol.36
, pp. 1116-1122
-
-
Ponstingl, H.1
Kabir, T.2
Thornton, J.M.3
-
33
-
-
0030623823
-
Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential
-
Bahar I, Atilgan AR, Erman B. Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential. Fold Des 1997;2:173-181.
-
(1997)
Fold Des
, vol.2
, pp. 173-181
-
-
Bahar, I.1
Atilgan, A.R.2
Erman, B.3
-
35
-
-
0035996990
-
Dynamics of proteins in crystals: Comparison of experiment with simple models
-
Kundu S, Melton JS, Sorensen DC, Phillips GN, Jr. Dynamics of proteins in crystals: comparison of experiment with simple models. Biophys J 2002;83:723-732.
-
(2002)
Biophys J
, vol.83
, pp. 723-732
-
-
Kundu, S.1
Melton, J.S.2
Sorensen, D.C.3
Phillips Jr., G.N.4
-
37
-
-
0024621473
-
Chain dimensions and fluctuations in random elastomeric networks. I. Phantom Guassian network in the undeformed state
-
Kloczkowski A, Mark JE, Erman B. Chain dimensions and fluctuations in random elastomeric networks. I. Phantom Guassian network in the undeformed state. Macromolecules 1989;22:1423-1432.
-
(1989)
Macromolecules
, vol.22
, pp. 1423-1432
-
-
Kloczkowski, A.1
Mark, J.E.2
Erman, B.3
-
38
-
-
0000496772
-
Vibrational dynamics of folded proteins: Significance of slow and fast motions in relation to function and stability
-
Bahar I, Atilgan AR, Demirel MC, Erman B. Vibrational dynamics of folded proteins: significance of slow and fast motions in relation to function and stability. Phys Rev Lett 1998;80:2733-2736.
-
(1998)
Phys Rev Lett
, vol.80
, pp. 2733-2736
-
-
Bahar, I.1
Atilgan, A.R.2
Demirel, M.C.3
Erman, B.4
-
39
-
-
39749099008
-
-
Hubbard SJ, Thornton JM. NACCESS. London: Department of Biochemistry and Molecular Biology, University College London; 1993.
-
Hubbard SJ, Thornton JM. NACCESS. London: Department of Biochemistry and Molecular Biology, University College London; 1993.
-
-
-
|