-
1
-
-
0032553012
-
RT loop flexibility enhances the specificity of Src family SH3 domains for HIV-1 Nef
-
Arold S., O'Brien R., Franken P., Strub M., Hoh F., Dumas C., and Ladbury J. RT loop flexibility enhances the specificity of Src family SH3 domains for HIV-1 Nef. Biochemistry 37 (1998) 14683-14691
-
(1998)
Biochemistry
, vol.37
, pp. 14683-14691
-
-
Arold, S.1
O'Brien, R.2
Franken, P.3
Strub, M.4
Hoh, F.5
Dumas, C.6
Ladbury, J.7
-
2
-
-
0037470616
-
Increased backbone mobility in β-barrel enhances entropy gain driving binding of n-timp-1 to mmp-3
-
Arumugam S., Gao G., Patton B.L., Semenchenko V., Brew K., and Van Doren S.R. Increased backbone mobility in β-barrel enhances entropy gain driving binding of n-timp-1 to mmp-3. J. Mol. Biol. 327 (2003) 719-734
-
(2003)
J. Mol. Biol.
, vol.327
, pp. 719-734
-
-
Arumugam, S.1
Gao, G.2
Patton, B.L.3
Semenchenko, V.4
Brew, K.5
Van Doren, S.R.6
-
3
-
-
0016828929
-
Dynamics of ligand binding to myoglobin
-
Austin R., Beeson K., Eisenstein L., Frauenfelder H., and Gunsalus I. Dynamics of ligand binding to myoglobin. Biochemistry 14 (1975) 5355-5373
-
(1975)
Biochemistry
, vol.14
, pp. 5355-5373
-
-
Austin, R.1
Beeson, K.2
Eisenstein, L.3
Frauenfelder, H.4
Gunsalus, I.5
-
4
-
-
4043156208
-
Direct determination of vibrational density of states change on ligand binding to a protein
-
Balog E., Becker T., Oettl M., Lechner R., Daniel R., Finney J., and Smith J. Direct determination of vibrational density of states change on ligand binding to a protein. Phys. Rev. Lett. 93 (2004) 028103
-
(2004)
Phys. Rev. Lett.
, vol.93
, pp. 028103
-
-
Balog, E.1
Becker, T.2
Oettl, M.3
Lechner, R.4
Daniel, R.5
Finney, J.6
Smith, J.7
-
5
-
-
0037628610
-
Total chemical synthesis of a functional interacting protein pair: the protooncogene H-Ras and the Ras-binding domain of its effector c-Raf1
-
Becker C., Hunter C., Seidel R., Kent S., Goody R., and Engelhard M. Total chemical synthesis of a functional interacting protein pair: the protooncogene H-Ras and the Ras-binding domain of its effector c-Raf1. Proc. Natl. Acad. Sci. USA 100 (2003) 5075-5080
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 5075-5080
-
-
Becker, C.1
Hunter, C.2
Seidel, R.3
Kent, S.4
Goody, R.5
Engelhard, M.6
-
6
-
-
33750587438
-
Molecular dynamics with coupling to an external heat bath
-
Berendsen H., Postma J., Van Gunsteren W., DiNola A., and Haak J. Molecular dynamics with coupling to an external heat bath. J. Chem. Phys. 81 (1984) 3684-3690
-
(1984)
J. Chem. Phys.
, vol.81
, pp. 3684-3690
-
-
Berendsen, H.1
Postma, J.2
Van Gunsteren, W.3
DiNola, A.4
Haak, J.5
-
7
-
-
0032966864
-
Antigen recognition by conformational selection
-
Berger C., Weber-Bornhauser S., Eggenberger J., Hanes J., Pluckthun A., and Bosshard H. Antigen recognition by conformational selection. FEBS Lett. 450 (1999) 149-153
-
(1999)
FEBS Lett.
, vol.450
, pp. 149-153
-
-
Berger, C.1
Weber-Bornhauser, S.2
Eggenberger, J.3
Hanes, J.4
Pluckthun, A.5
Bosshard, H.6
-
8
-
-
0032897494
-
An analysis of conformational changes on protein-protein association: implications for predictive docking
-
Betts M., and Sternberg M. 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.1
Sternberg, M.2
-
9
-
-
0028014642
-
Bound water molecules and conformational stabilization help mediate an antigen-antibody association
-
Bhat T., Bentley G., Boulot G., Greene M., Tello D., Dall'Acqua W., Souchon H., Schwarz F., Mariuzza R., and Poljak R. Bound water molecules and conformational stabilization help mediate an antigen-antibody association. Proc. Natl. Acad. Sci. USA 91 (1994) 1089-1093
-
(1994)
Proc. Natl. Acad. Sci. USA
, vol.91
, pp. 1089-1093
-
-
Bhat, T.1
Bentley, G.2
Boulot, G.3
Greene, M.4
Tello, D.5
Dall'Acqua, W.6
Souchon, H.7
Schwarz, F.8
Mariuzza, R.9
Poljak, R.10
-
10
-
-
0035432947
-
Molecular recognition by induced fit: how fit is the concept?
-
Bosshard H. Molecular recognition by induced fit: how fit is the concept?. News Physiol. Sci. 16 (2001) 171-173
-
(2001)
News Physiol. Sci.
, vol.16
, pp. 171-173
-
-
Bosshard, H.1
-
11
-
-
25444532318
-
Identification of slow correlated motions in proteins using residual dipolar and hydrogen-bondscalar couplings
-
Bouvignies G., Bernado P., Meier S., Cho K., Grzesiek S., Bruschweiler R., and Blackledge M. Identification of slow correlated motions in proteins using residual dipolar and hydrogen-bondscalar couplings. Proc. Natl. Acad. Sci. USA 102 (2005) 13885-13890
-
(2005)
Proc. Natl. Acad. Sci. USA
, vol.102
, pp. 13885-13890
-
-
Bouvignies, G.1
Bernado, P.2
Meier, S.3
Cho, K.4
Grzesiek, S.5
Bruschweiler, R.6
Blackledge, M.7
-
12
-
-
0030961726
-
Entropy in protein folding and in protein-protein interactions
-
Brady G., and Sharp K. Entropy in protein folding and in protein-protein interactions. Curr. Opin. Struct. Biol. 7 (1997) 215-221
-
(1997)
Curr. Opin. Struct. Biol.
, vol.7
, pp. 215-221
-
-
Brady, G.1
Sharp, K.2
-
14
-
-
1542465044
-
Organization and functions of interacting domains for signaling by protein-protein interactions
-
Buck E., and Iyengar R. Organization and functions of interacting domains for signaling by protein-protein interactions. Sci. STKE 2003 (2003) re14
-
(2003)
Sci. STKE
, vol.2003
-
-
Buck, E.1
Iyengar, R.2
-
15
-
-
0028331255
-
Normal mode analysis of protein dynamics
-
Case D. Normal mode analysis of protein dynamics. Curr. Opin. Struct. Biol. 4 (1994) 285-290
-
(1994)
Curr. Opin. Struct. Biol.
, vol.4
, pp. 285-290
-
-
Case, D.1
-
16
-
-
0031910020
-
Locally accessible conformations of proteins: multiple molecular dynamics simulations of crambin
-
Caves L., Evanseck J., and Karplus M. Locally accessible conformations of proteins: multiple molecular dynamics simulations of crambin. Protein Sci. 7 (1998) 649-666
-
(1998)
Protein Sci.
, vol.7
, pp. 649-666
-
-
Caves, L.1
Evanseck, J.2
Karplus, M.3
-
17
-
-
33645961739
-
A smooth particle mesh Ewald method
-
Essmann U., Perera L., Berkowitz M., Darden T., Lee H., and Pedersen L. A smooth particle mesh Ewald method. J. Chem. Phys. B 103 (1995) 6998-7014
-
(1995)
J. Chem. Phys. B
, vol.103
, pp. 6998-7014
-
-
Essmann, U.1
Perera, L.2
Berkowitz, M.3
Darden, T.4
Lee, H.5
Pedersen, L.6
-
18
-
-
0038509001
-
Induction of flexibility through protein-protein interactions
-
Fayos R., Melacini G., Newlon M., Burns L., Scott J., and Jennings P. Induction of flexibility through protein-protein interactions. J. Biol. Chem. 278 (2003) 18581-18587
-
(2003)
J. Biol. Chem.
, vol.278
, pp. 18581-18587
-
-
Fayos, R.1
Melacini, G.2
Newlon, M.3
Burns, L.4
Scott, J.5
Jennings, P.6
-
19
-
-
5144223810
-
Bulk-solvent and hydration-shell fluctuations, similar to α- and β-fluctuations in glasses, control protein motions and functions
-
Fenimore P., Frauenfelder H., McMahon B., and Young R. Bulk-solvent and hydration-shell fluctuations, similar to α- and β-fluctuations in glasses, control protein motions and functions. Proc. Natl. Acad. Sci. USA 101 (2004) 14408-14413
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, pp. 14408-14413
-
-
Fenimore, P.1
Frauenfelder, H.2
McMahon, B.3
Young, R.4
-
20
-
-
0036385729
-
Side-chain dynamics of the SAP SH2 domain correlate with a binding hot spot and a region with conformational plasticity
-
Finerty Jr. P.J., Muhandiram R., and Forman-Kay J.D. Side-chain dynamics of the SAP SH2 domain correlate with a binding hot spot and a region with conformational plasticity. J. Mol. Biol. 322 (2002) 605-620
-
(2002)
J. Mol. Biol.
, vol.322
, pp. 605-620
-
-
Finerty Jr., P.J.1
Muhandiram, R.2
Forman-Kay, J.D.3
-
21
-
-
0024745871
-
The price of lost freedom: entropy of bimolecular complex formation
-
Finkelstein A., and Janin J. The price of lost freedom: entropy of bimolecular complex formation. Protein Eng. 3 (1989) 1-3
-
(1989)
Protein Eng.
, vol.3
, pp. 1-3
-
-
Finkelstein, A.1
Janin, J.2
-
22
-
-
0027943261
-
Conformational isomerism and the diversity of antibodies
-
Foote J., and Milstein C. Conformational isomerism and the diversity of antibodies. Proc. Natl. Acad. Sci. USA 91 (1994) 10370-10374
-
(1994)
Proc. Natl. Acad. Sci. USA
, vol.91
, pp. 10370-10374
-
-
Foote, J.1
Milstein, C.2
-
23
-
-
0032756923
-
The 'dynamics' in the thermodynamics of binding
-
Forman-Kay J.D. The 'dynamics' in the thermodynamics of binding. Nat. Struct. Biol. 6 (1999) 1086-1087
-
(1999)
Nat. Struct. Biol.
, vol.6
, pp. 1086-1087
-
-
Forman-Kay, J.D.1
-
24
-
-
0031708076
-
The energy landscape in non-biological and biological molecules
-
Frauenfelder H., and Leeson D. The energy landscape in non-biological and biological molecules. Nat. Struct. Biol. 5 (1998) 757-759
-
(1998)
Nat. Struct. Biol.
, vol.5
, pp. 757-759
-
-
Frauenfelder, H.1
Leeson, D.2
-
25
-
-
0031552366
-
Thermodynamics of the interaction of barnase and barstar: changes in free energy versus changes in enthalpy on mutation
-
Frisch C., Schreiber G., Johnson C., and Fersht A. Thermodynamics of the interaction of barnase and barstar: changes in free energy versus changes in enthalpy on mutation. J. Mol. Biol. 267 (1997) 696-706
-
(1997)
J. Mol. Biol.
, vol.267
, pp. 696-706
-
-
Frisch, C.1
Schreiber, G.2
Johnson, C.3
Fersht, A.4
-
26
-
-
0037397987
-
Peptide folding simulations
-
Gnanakaran S., Nymeyer H., Portman J., Sanbonmatsu K., and Garcia A. Peptide folding simulations. Curr. Opin. Struct. Biol. 13 (2003) 168-174
-
(2003)
Curr. Opin. Struct. Biol.
, vol.13
, pp. 168-174
-
-
Gnanakaran, S.1
Nymeyer, H.2
Portman, J.3
Sanbonmatsu, K.4
Garcia, A.5
-
27
-
-
0347602124
-
Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf
-
Gohlke H., and Case D. Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf. J. Comput. Chem. 25 (2004) 238-250
-
(2004)
J. Comput. Chem.
, vol.25
, pp. 238-250
-
-
Gohlke, H.1
Case, D.2
-
28
-
-
0043245780
-
Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RalGDS complexes
-
Gohlke H., Kiel C., and Case D. Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RalGDS complexes. J. Mol. Biol. 330 (2003) 891-913
-
(2003)
J. Mol. Biol.
, vol.330
, pp. 891-913
-
-
Gohlke, H.1
Kiel, C.2
Case, D.3
-
29
-
-
0026665439
-
Fuzzy cluster analysis of molecular dynamics trajectories
-
Gordon H., and Somorjai R. Fuzzy cluster analysis of molecular dynamics trajectories. Proteins 14 (1992) 249-264
-
(1992)
Proteins
, vol.14
, pp. 249-264
-
-
Gordon, H.1
Somorjai, R.2
-
30
-
-
9944237833
-
Complementarity of structure ensembles in protein-protein binding
-
Grünberg R., Leckner J., and Nilges M. Complementarity of structure ensembles in protein-protein binding. Structure (Camb) 12 (2004) 2125-2136
-
(2004)
Structure (Camb)
, vol.12
, pp. 2125-2136
-
-
Grünberg, R.1
Leckner, J.2
Nilges, M.3
-
31
-
-
18144399340
-
Replica-exchange Monte Carlo scheme for bayesian data analysis
-
Habeck M., Nilges M., and Rieping W. Replica-exchange Monte Carlo scheme for bayesian data analysis. Phys. Rev. Lett. 94 (2005) 018105
-
(2005)
Phys. Rev. Lett.
, vol.94
, pp. 018105
-
-
Habeck, M.1
Nilges, M.2
Rieping, W.3
-
32
-
-
0032536446
-
Conformational correction mechanisms aiding antigen recognition by a humanized antibody
-
Holmes M., Buss T., and Foote J. Conformational correction mechanisms aiding antigen recognition by a humanized antibody. J. Exp. Med. 187 (1998) 479-485
-
(1998)
J. Exp. Med.
, vol.187
, pp. 479-485
-
-
Holmes, M.1
Buss, T.2
Foote, J.3
-
33
-
-
0030442990
-
Positioning hydrogen atoms by optimizing hydrogen-bond networks in protein structures
-
Hooft R., Sander C., and Vriend G. Positioning hydrogen atoms by optimizing hydrogen-bond networks in protein structures. Proteins 26 (1996) 363-376
-
(1996)
Proteins
, vol.26
, pp. 363-376
-
-
Hooft, R.1
Sander, C.2
Vriend, G.3
-
34
-
-
11244302391
-
Entropy calculation of HIV-1 Env gp120, its receptor CD4 and their complex: an analysis of configurational entropy changes upon complexation
-
Hsu S., Peter C., van Gunsteren W., and Bonvin A. Entropy calculation of HIV-1 Env gp120, its receptor CD4 and their complex: an analysis of configurational entropy changes upon complexation. Biophys. J. 88 (2004) 15-24
-
(2004)
Biophys. J.
, vol.88
, pp. 15-24
-
-
Hsu, S.1
Peter, C.2
van Gunsteren, W.3
Bonvin, A.4
-
35
-
-
0029019869
-
A continuum model for protein-protein interactions: application to the docking problem
-
Jackson R., and Sternberg M. A continuum model for protein-protein interactions: application to the docking problem. J. Mol. Biol. 250 (1995) 258-275
-
(1995)
J. Mol. Biol.
, vol.250
, pp. 258-275
-
-
Jackson, R.1
Sternberg, M.2
-
36
-
-
24644521419
-
Structure and kinetics of a transient antibody binding intermediate reveal a kinetic discrimination mechanism in antigen recognition
-
James L., and Tawfik D. Structure and kinetics of a transient antibody binding intermediate reveal a kinetic discrimination mechanism in antigen recognition. Proc. Natl. Acad. Sci. USA 102 (2005) 12730-12735
-
(2005)
Proc. Natl. Acad. Sci. USA
, vol.102
, pp. 12730-12735
-
-
James, L.1
Tawfik, D.2
-
37
-
-
0028861437
-
Elusive affinities
-
Janin J. Elusive affinities. Proteins 21 (1995) 30-39
-
(1995)
Proteins
, vol.21
, pp. 30-39
-
-
Janin, J.1
-
38
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
Jorgensen W.L., Chandrasekhar J., Madura J.D., Impey R.W., and Klein M.L. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79 (1983) 926-935
-
(1983)
J. Chem. Phys.
, vol.79
, pp. 926-935
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Madura, J.D.3
Impey, R.W.4
Klein, M.L.5
-
39
-
-
0346220393
-
The role of dynamics in allosteric regulation
-
Kern D., and Zuiderweg E.R. The role of dynamics in allosteric regulation. Curr. Opin. Struct. Biol. 13 (2003) 748-757
-
(2003)
Curr. Opin. Struct. Biol.
, vol.13
, pp. 748-757
-
-
Kern, D.1
Zuiderweg, E.R.2
-
40
-
-
0001195192
-
The binding of nicotinamide adenine dinucleotide to yeast glyceraldehyde-3-phosphate dehydrogenase: temperature-jump relaxation studies on the mechanism of an allosteric enzyme
-
Kirschner K., Eigen M., Bittman R., and Voigt B. The binding of nicotinamide adenine dinucleotide to yeast glyceraldehyde-3-phosphate dehydrogenase: temperature-jump relaxation studies on the mechanism of an allosteric enzyme. Proc. Natl. Acad. Sci. USA 56 (1966) 1661-1667
-
(1966)
Proc. Natl. Acad. Sci. USA
, vol.56
, pp. 1661-1667
-
-
Kirschner, K.1
Eigen, M.2
Bittman, R.3
Voigt, B.4
-
41
-
-
0032374086
-
Energy landscape of a native protein: jumping-among-minima model
-
Kitao A., Hayward S., and Go N. Energy landscape of a native protein: jumping-among-minima model. Proteins 33 (1998) 496-517
-
(1998)
Proteins
, vol.33
, pp. 496-517
-
-
Kitao, A.1
Hayward, S.2
Go, N.3
-
42
-
-
0001858251
-
Application of a theory of enzyme specifity to protein synthesis
-
Koshland D. Application of a theory of enzyme specifity 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.1
-
43
-
-
0033970020
-
Folding and binding cascades: dynamic landscapes and population shifts
-
Kumar S., Ma B., Tsai C., 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.3
Sinha, N.4
Nussinov, R.5
-
44
-
-
0037438461
-
The basis of the hydrophobic effect
-
Kyte J. The basis of the hydrophobic effect. Biophys. Chem. 100 (2003) 193-203
-
(2003)
Biophys. Chem.
, vol.100
, pp. 193-203
-
-
Kyte, J.1
-
45
-
-
0001039702
-
Kinetic evidence for hapten-induced conformational transition in immunoglobin MOPC 460
-
Lancet D., and Pecht I. Kinetic evidence for hapten-induced conformational transition in immunoglobin MOPC 460. Proc. Natl. Acad. Sci. USA 73 (1976) 3549-3553
-
(1976)
Proc. Natl. Acad. Sci. USA
, vol.73
, pp. 3549-3553
-
-
Lancet, D.1
Pecht, I.2
-
46
-
-
0029561993
-
Spectroscopic, calorimetric, and kinetic demonstration of conformational adaptation in peptide-antibody recognition
-
Leder L., Berger C., Bornhauser S., Wendt H., Ackermann F., Jelesarov I., and Bosshard H. Spectroscopic, calorimetric, and kinetic demonstration of conformational adaptation in peptide-antibody recognition. Biochemistry 34 (1995) 16509-16518
-
(1995)
Biochemistry
, vol.34
, pp. 16509-16518
-
-
Leder, L.1
Berger, C.2
Bornhauser, S.3
Wendt, H.4
Ackermann, F.5
Jelesarov, I.6
Bosshard, H.7
-
47
-
-
0033988897
-
Redistribution and loss of side chain entropy upon formation of a calmodulinpeptide complex
-
Lee A., Kinnear S., and Wand A. Redistribution and loss of side chain entropy upon formation of a calmodulinpeptide complex. Nat. Struct. Biol. 7 (2000) 72-77
-
(2000)
Nat. Struct. Biol.
, vol.7
, pp. 72-77
-
-
Lee, A.1
Kinnear, S.2
Wand, A.3
-
48
-
-
13444301037
-
A survey of flexible protein binding mechanisms and their transition states using native topology based energy landscapes
-
Levy Y., Cho S., Onuchic J., and Wolynes P. A survey of flexible protein binding mechanisms and their transition states using native topology based energy landscapes. J. Mol. Biol. 346 (2005) 1121-1145
-
(2005)
J. Mol. Biol.
, vol.346
, pp. 1121-1145
-
-
Levy, Y.1
Cho, S.2
Onuchic, J.3
Wolynes, P.4
-
49
-
-
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
-
50
-
-
0035901519
-
An increase in side chain entropy facilitates effector binding: nmr characterization of the side chain methyl group dynamics in cdc42hs
-
Loh A.P., Pawley N., Nicholson L.K., and Oswald R.E. An increase in side chain entropy facilitates effector binding: nmr characterization of the side chain methyl group dynamics in cdc42hs. Biochemistry 40 (2001) 4590-4600
-
(2001)
Biochemistry
, vol.40
, pp. 4590-4600
-
-
Loh, A.P.1
Pawley, N.2
Nicholson, L.K.3
Oswald, R.E.4
-
51
-
-
0037495965
-
Development of polyphosphate parameters for use with the AMBER force field
-
Meagher K., Redman L., and Carlson H. Development of polyphosphate parameters for use with the AMBER force field. J. Comput. Chem. 24 (2003) 1016-1025
-
(2003)
J. Comput. Chem.
, vol.24
, pp. 1016-1025
-
-
Meagher, K.1
Redman, L.2
Carlson, H.3
-
52
-
-
0035964181
-
Structure, dynamics, and thermodynamics of the structural domain of troponin C in complex with the regulatory peptide 1-40 of troponin I
-
Mercier P., Spyracopoulos L., and Sykes B. Structure, dynamics, and thermodynamics of the structural domain of troponin C in complex with the regulatory peptide 1-40 of troponin I. Biochemistry 40 (2001) 10063-10077
-
(2001)
Biochemistry
, vol.40
, pp. 10063-10077
-
-
Mercier, P.1
Spyracopoulos, L.2
Sykes, B.3
-
53
-
-
25844507555
-
The entropic cost of protein-protein association: a case study on acetylcholinesterase binding to fasciculin-2
-
Minh D.D., Bui J.M., Chang C.E., Jain T., Swanson J.M., and McCammon J.A. The entropic cost of protein-protein association: a case study on acetylcholinesterase binding to fasciculin-2. Biophys. J. 89 (2005) L25-L27
-
(2005)
Biophys. J.
, vol.89
-
-
Minh, D.D.1
Bui, J.M.2
Chang, C.E.3
Jain, T.4
Swanson, J.M.5
McCammon, J.A.6
-
54
-
-
78651189765
-
On the nature of allosteric transitions: a plausible model
-
Monod J., Wyman J., and Changeux J. 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.3
-
55
-
-
0034900495
-
Free energy decomposition of protein-protein interactions
-
Noskov S.Y., and Lim C. Free energy decomposition of protein-protein interactions. Biophys. J. 81 (2001) 737-750
-
(2001)
Biophys. J.
, vol.81
, pp. 737-750
-
-
Noskov, S.Y.1
Lim, C.2
-
56
-
-
0031001259
-
Changes in the NMR-derived motional parameters of the insulin receptor substrate 1 phosphotyrosine binding domain upon binding to an interleukin 4 receptor phosphopeptide
-
Olejniczak E.T., Zhou M.M., and Fesik S.W. Changes in the NMR-derived motional parameters of the insulin receptor substrate 1 phosphotyrosine binding domain upon binding to an interleukin 4 receptor phosphopeptide. Biochemistry 36 (1997) 4118-4124
-
(1997)
Biochemistry
, vol.36
, pp. 4118-4124
-
-
Olejniczak, E.T.1
Zhou, M.M.2
Fesik, S.W.3
-
57
-
-
0029633186
-
AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules
-
Pearlman D., Case D., Caldwell J., Ross W., Cheatham III T., DeBolt S., Ferguson D., Seibel G., and Kollman P. AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules. Comp. Phys. Commun. 91 (1995) 1-41
-
(1995)
Comp. Phys. Commun.
, vol.91
, pp. 1-41
-
-
Pearlman, D.1
Case, D.2
Caldwell, J.3
Ross, W.4
Cheatham III, T.5
DeBolt, S.6
Ferguson, D.7
Seibel, G.8
Kollman, P.9
-
58
-
-
0024199422
-
Stability of protein structure and hydrophobic interaction
-
Privalov P.L., and Gill S.J. Stability of protein structure and hydrophobic interaction. Adv. Protein Chem. 39 (1988) 191-234
-
(1988)
Adv. Protein Chem.
, vol.39
, pp. 191-234
-
-
Privalov, P.L.1
Gill, S.J.2
-
59
-
-
0026416668
-
Reconciling the magnitude of the microscopic and macroscopic hydrophobic effects
-
Sharp K., Nicholls A., Fine R., and Honig B. Reconciling the magnitude of the microscopic and macroscopic hydrophobic effects. Science 252 (1991) 106-109
-
(1991)
Science
, vol.252
, pp. 106-109
-
-
Sharp, K.1
Nicholls, A.2
Fine, R.3
Honig, B.4
-
60
-
-
0034255123
-
Speeding molecular recognition by using the folding funnel: the fly-casting mechanism
-
Shoemaker B., Portman J., and Wolynes P. Speeding molecular recognition by using the folding funnel: the fly-casting mechanism. Proc. Natl. Acad. Sci. USA 97 (2000) 8868-8873
-
(2000)
Proc. Natl. Acad. Sci. USA
, vol.97
, pp. 8868-8873
-
-
Shoemaker, B.1
Portman, J.2
Wolynes, P.3
-
61
-
-
0001666112
-
Entropy changes accompanying association reactions of proteins
-
Steinberg I.Z., and Scheraga H.A. Entropy changes accompanying association reactions of proteins. J. Biol. Chem. 238 (1963) 172-181
-
(1963)
J. Biol. Chem.
, vol.238
, pp. 172-181
-
-
Steinberg, I.Z.1
Scheraga, H.A.2
-
62
-
-
0030299991
-
15N NMR relaxation studies of free and inhibitor-bound 4-oxalocrotonate tautomerase: backbone dynamics and entropy changes of an enzyme upon inhibitor binding
-
Stivers J.T., Abeygunawardana C., Mildvan A.S., and Whitman C.P. 15N NMR relaxation studies of free and inhibitor-bound 4-oxalocrotonate tautomerase: backbone dynamics and entropy changes of an enzyme upon inhibitor binding. Biochemistry 35 (1996) 16036-16047
-
(1996)
Biochemistry
, vol.35
, pp. 16036-16047
-
-
Stivers, J.T.1
Abeygunawardana, C.2
Mildvan, A.S.3
Whitman, C.P.4
-
63
-
-
0034687780
-
Estimation of the hydrophobic effect in an antigen-antibody protein-protein interface
-
Sundberg E., Urrutia M., Braden B., Isern J., Tsuchiya D., Fields B., Malchiodi E., Tormo J., Schwarz F., and Mariuzza R. Estimation of the hydrophobic effect in an antigen-antibody protein-protein interface. Biochemistry 39 (2000) 15375-15387
-
(2000)
Biochemistry
, vol.39
, pp. 15375-15387
-
-
Sundberg, E.1
Urrutia, M.2
Braden, B.3
Isern, J.4
Tsuchiya, D.5
Fields, B.6
Malchiodi, E.7
Tormo, J.8
Schwarz, F.9
Mariuzza, R.10
-
64
-
-
0000118827
-
Harmonic and quasiharmonic descriptions of crambin
-
Teeter M., and Case D. Harmonic and quasiharmonic descriptions of crambin. J. Phys. Chem. 94 (1990) 8091-8097
-
(1990)
J. Phys. Chem.
, vol.94
, pp. 8091-8097
-
-
Teeter, M.1
Case, D.2
-
65
-
-
0028360307
-
The contribution of vibrational entropy to molecular association. The dimerization of insulin
-
Tidor B., and Karplus M. The contribution of vibrational entropy to molecular association. The dimerization of insulin. J. Mol. Biol. 238 (1994) 405-414
-
(1994)
J. Mol. Biol.
, vol.238
, pp. 405-414
-
-
Tidor, B.1
Karplus, M.2
-
66
-
-
0037197254
-
Novel computer program for fast exact calculation of accessible and molecular surface areas and average surface curvature
-
Tsodikov O.V., Record Jr. M.T., and Sergeev Y.V. Novel computer program for fast exact calculation of accessible and molecular surface areas and average surface curvature. J. Comput. Chem. 23 (2002) 600-609
-
(2002)
J. Comput. Chem.
, vol.23
, pp. 600-609
-
-
Tsodikov, O.V.1
Record Jr., M.T.2
Sergeev, Y.V.3
-
67
-
-
84946450438
-
Algorithms for macromolecular dynamics and constraint dynamics
-
van Gunsteren W., and Berendsen H. Algorithms for macromolecular dynamics and constraint dynamics. Mol. Phys. 34 (1977) 1311-1327
-
(1977)
Mol. Phys.
, vol.34
, pp. 1311-1327
-
-
van Gunsteren, W.1
Berendsen, H.2
-
68
-
-
0034646179
-
Backbone dynamics of Tet repressor alpha8intersectionalpha9 loop
-
Vergani B., Kintrup M., Hillen W., Lami H., Piemont E., Bombarda E., Alberti P., Doglia S.M., and Chabbert M. Backbone dynamics of Tet repressor alpha8intersectionalpha9 loop. Biochemistry 39 (2000) 2759-2768
-
(2000)
Biochemistry
, vol.39
, pp. 2759-2768
-
-
Vergani, B.1
Kintrup, M.2
Hillen, W.3
Lami, H.4
Piemont, E.5
Bombarda, E.6
Alberti, P.7
Doglia, S.M.8
Chabbert, M.9
-
69
-
-
0036841606
-
Numerical study of the entropy loss of dimerization and the folding thermodynamics of the GCN4 leucine zipper
-
Viñals J., Kolinski A., and Skolnick J. Numerical study of the entropy loss of dimerization and the folding thermodynamics of the GCN4 leucine zipper. Biophys. J. 83 (2002) 2801-2811
-
(2002)
Biophys. J.
, vol.83
, pp. 2801-2811
-
-
Viñals, J.1
Kolinski, A.2
Skolnick, J.3
-
70
-
-
0035798419
-
The role of backbone motions in ligand binding to the c-Src SH3 domain
-
Wang C., Pawley N., and Nicholson L. The role of backbone motions in ligand binding to the c-Src SH3 domain. J. Mol. Biol. 313 (2001) 873-887
-
(2001)
J. Mol. Biol.
, vol.313
, pp. 873-887
-
-
Wang, C.1
Pawley, N.2
Nicholson, L.3
-
71
-
-
0001398008
-
How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?
-
Wang J., Cieplak P., and Kollman P. How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?. J. Comput. Chem. 22 (2000) 1048-1074
-
(2000)
J. Comput. Chem.
, vol.22
, pp. 1048-1074
-
-
Wang, J.1
Cieplak, P.2
Kollman, P.3
-
72
-
-
0029764317
-
Backbone dynamics of the C-terminal domain of Escherichia coli topoisomerase I in the absence and presence of single-stranded DNA
-
Yu L., Zhu C.X., Tse-Dinh Y.C., and Fesik S.W. Backbone dynamics of the C-terminal domain of Escherichia coli topoisomerase I in the absence and presence of single-stranded DNA. Biochemistry 35 (1996) 9661-9666
-
(1996)
Biochemistry
, vol.35
, pp. 9661-9666
-
-
Yu, L.1
Zhu, C.X.2
Tse-Dinh, Y.C.3
Fesik, S.W.4
-
73
-
-
0035799320
-
15N NMR relaxation studies of backbone dynamics in free and steroid-bound Delta 5-3-ketosteroid isomerase from Pseudomonas testosteroni
-
Yun S., Jang D.S., Kim D.H., Choi K.Y., and Lee H.C. 15N NMR relaxation studies of backbone dynamics in free and steroid-bound Delta 5-3-ketosteroid isomerase from Pseudomonas testosteroni. Biochemistry 40 (2001) 3967-3973
-
(2001)
Biochemistry
, vol.40
, pp. 3967-3973
-
-
Yun, S.1
Jang, D.S.2
Kim, D.H.3
Choi, K.Y.4
Lee, H.C.5
-
74
-
-
0035822676
-
Dynamics of the Mrf-2 DNA-binding domain free and in complex with DNA
-
Zhu L., Hu J., Lin D., Whitson R., Itakura K., and Chen Y. Dynamics of the Mrf-2 DNA-binding domain free and in complex with DNA. Biochemistry 40 (2001) 9142-9150
-
(2001)
Biochemistry
, vol.40
, pp. 9142-9150
-
-
Zhu, L.1
Hu, J.2
Lin, D.3
Whitson, R.4
Itakura, K.5
Chen, Y.6
-
75
-
-
0032710610
-
Increased protein backbone conformational entropy upon hydrophobic ligand binding
-
Zidek L., Novotny M.V., and Stone M.J. Increased protein backbone conformational entropy upon hydrophobic ligand binding. Nat. Struct. Biol. 6 (1999) 1118-1121
-
(1999)
Nat. Struct. Biol.
, vol.6
, pp. 1118-1121
-
-
Zidek, L.1
Novotny, M.V.2
Stone, M.J.3
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