-
1
-
-
0033954256
-
The Protein Data Bank
-
Berman, H. M., J. Westbrook, Z. Feng, G. Gillirand, T. N. Bhat, H. Weissig, I. N. Shindyalov, and P. E. Bourne. 2000. The Protein Data Bank, Nucleic Acids Res. 28:235-242.
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Gillirand, G.4
Bhat, T.N.5
Weissig, H.6
Shindyalov, I.N.7
Bourne, P.E.8
-
2
-
-
0036424048
-
Transition path sampling: Throwing ropes over rough mountain passes, in the dark
-
Bolhuis, P. G., D. Chandler, C. Dellago, and P. L. Geissler. 2002. Transition path sampling: throwing ropes over rough mountain passes, in the dark. Annu. Rev. Phys. Chem. 53:291-318.
-
(2002)
Annu. Rev. Phys. Chem.
, vol.53
, pp. 291-318
-
-
Bolhuis, P.G.1
Chandler, D.2
Dellago, C.3
Geissler, P.L.4
-
3
-
-
0036183221
-
Im7 folding mechanism: Misfolding on a path to the native state
-
Capaldi, A. P., C. Kleanthous, and S. E. Radford. 2002. Im7 folding mechanism: misfolding on a path to the native state. Nat. Struct. Biol. 9:209-216.
-
(2002)
Nat. Struct. Biol.
, vol.9
, pp. 209-216
-
-
Capaldi, A.P.1
Kleanthous, C.2
Radford, S.E.3
-
4
-
-
0035943455
-
Four-body potentials reveal protein-specific correlations to stability changes caused by hydrophobic core mutations
-
Carter, C. W., B. C. LeFebvre, S. A. Cammer, A. Tropsha, and M. H. Edgell. 2001. Four-body potentials reveal protein-specific correlations to stability changes caused by hydrophobic core mutations. J. Mol. Biol. 311:625-638.
-
(2001)
J. Mol. Biol.
, vol.311
, pp. 625-638
-
-
Carter, C.W.1
LeFebvre, B.C.2
Cammer, S.A.3
Tropsha, A.4
Edgell, M.H.5
-
5
-
-
0032708771
-
Mutational analysis of acylphosphatase suggests the importance of topology and contact order in protein folding
-
Chiti, F., N. Taddei, P. M. White, M. Bucciantini, F. Magherini, M. Stefani, and C. M. Dobson. 1999. Mutational analysis of acylphosphatase suggests the importance of topology and contact order in protein folding. Nat. Struct. Biol. 6:1005-1009.
-
(1999)
Nat. Struct. Biol.
, vol.6
, pp. 1005-1009
-
-
Chiti, F.1
Taddei, N.2
White, P.M.3
Bucciantini, M.4
Magherini, F.5
Stefani, M.6
Dobson, C.M.7
-
6
-
-
0034685604
-
Topological and energetic factors: What determines the structural detail of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins
-
Clementi, C., H. Nymeyer, and J. N. Onuchic. 2000. Topological and energetic factors: what determines the structural detail of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins. J. Mol. Biol. 298:937-953.
-
(2000)
J. Mol. Biol.
, vol.298
, pp. 937-953
-
-
Clementi, C.1
Nymeyer, H.2
Onuchic, J.N.3
-
7
-
-
0036280655
-
Molecular dynamics simulations of the protein unfolding/folding reaction
-
Daggett, V. 2002. Molecular dynamics simulations of the protein unfolding/folding reaction. Acc. Chem. Res. 35:422-429.
-
(2002)
Acc. Chem. Res.
, vol.35
, pp. 422-429
-
-
Daggett, V.1
-
8
-
-
0037221599
-
Is there a unifying mechanism for protein folding?
-
Daggett, V., and A. R. Fersht. 2003. Is there a unifying mechanism for protein folding? Trends Biochem. Sci. 28:18-25.
-
(2003)
Trends Biochem. Sci.
, vol.28
, pp. 18-25
-
-
Daggett, V.1
Fersht, A.R.2
-
9
-
-
0009586942
-
Understanding protein folding via free-energy surfaces from theory and experiment
-
Dinner, A. R., A. Sali, L. J. Smith, C. M. Dobson, and M. Karplus. 2000. Understanding protein folding via free-energy surfaces from theory and experiment. Trends Biochem. Sci. 25:331-339.
-
(2000)
Trends Biochem. Sci.
, vol.25
, pp. 331-339
-
-
Dinner, A.R.1
Sali, A.2
Smith, L.J.3
Dobson, C.M.4
Karplus, M.5
-
10
-
-
0001563395
-
On the transition coordinate for protein folding
-
Du, R., V. S. Pande, A. Y. Grosberg, T. Tanaka, and E. I. Shakhnovich. 1998. On the transition coordinate for protein folding. J. Chem. Phys. 108:334-350.
-
(1998)
J. Chem. Phys.
, vol.108
, pp. 334-350
-
-
Du, R.1
Pande, V.S.2
Grosberg, A.Y.3
Tanaka, T.4
Shakhnovich, E.I.5
-
11
-
-
0037154980
-
Protein folding and unfolding at atomic resolution
-
Fersht, A. R., and V. Daggett. 2002. Protein folding and unfolding at atomic resolution. Cell. 108:573-582.
-
(2002)
Cell
, vol.108
, pp. 573-582
-
-
Fersht, A.R.1
Daggett, V.2
-
12
-
-
0026511656
-
The folding of an enzyme. I. Theory of protein engineering analysis of stability and pathway of protein folding
-
Fersht, A. R., A. Matouschek, and L. Serrano. 1992. The folding of an enzyme. I. Theory of protein engineering analysis of stability and pathway of protein folding. J. Mol. Biol. 224:771-782.
-
(1992)
J. Mol. Biol.
, vol.224
, pp. 771-782
-
-
Fersht, A.R.1
Matouschek, A.2
Serrano, L.3
-
13
-
-
0034984382
-
Mapping the folding pathway of an immunoglobulin domain: Structural detail from Φ value analysis and movement of the transition state
-
Fowler, S. B., and J. Clarke. 2001. Mapping the folding pathway of an immunoglobulin domain: structural detail from Φ value analysis and movement of the transition state. Structure. 9:355-366.
-
(2001)
Structure
, vol.9
, pp. 355-366
-
-
Fowler, S.B.1
Clarke, J.2
-
14
-
-
0036084144
-
ProTherm, thermodynamic database for proteins and mutants: Developments in version 3.0
-
Gromiha, M. M., H. Uedaira, J. An, S. Selvaraj, P. Prabakaran, and A. Sarai. 2002. ProTherm, thermodynamic database for proteins and mutants: developments in version 3.0. Nucleic Acids Res. 30:301-302.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 301-302
-
-
Gromiha, M.M.1
Uedaira, H.2
An, J.3
Selvaraj, S.4
Prabakaran, P.5
Sarai, A.6
-
15
-
-
0037076334
-
Molecular dynamics simulations of protein folding from the transition state
-
Gsponer, J., and A. Caflisch. 2002. Molecular dynamics simulations of protein folding from the transition state. Proc. Natl. Acad. Sci. USA. 99:6719-6724.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 6719-6724
-
-
Gsponer, J.1
Caflisch, A.2
-
16
-
-
0036291145
-
Predicting changes in the stability of proteins and protein complexes: A study of more than 1000 mutations
-
Guerois, R., J. E. Nielsen, and L. Serrano. 2002. Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations. J. Mol. Biol. 320:369-387.
-
(2002)
J. Mol. Biol.
, vol.320
, pp. 369-387
-
-
Guerois, R.1
Nielsen, J.E.2
Serrano, L.3
-
17
-
-
0034677663
-
The folding of an immunoglobulin-like Greek key protein is defined by a common-core nucleus and regions constrained by topology
-
Hamill, S. J., A. Steward, and J. Clarke. 2000. The folding of an immunoglobulin-like Greek key protein is defined by a common-core nucleus and regions constrained by topology. J. Mol. Biol. 297:165-178.
-
(2000)
J. Mol. Biol.
, vol.297
, pp. 165-178
-
-
Hamill, S.J.1
Steward, A.2
Clarke, J.3
-
18
-
-
0028868995
-
The structure of the transition state for folding of chymotrypsin inhibitor 2 analysed by protein engineering methods: Evidence for a nucleation-condensation mechanism for protein folding
-
Itzhaki, L. S., D. E. Otzen, and A. R. Fersht. 1995. The structure of the transition state for folding of chymotrypsin inhibitor 2 analysed by protein engineering methods: evidence for a nucleation-condensation mechanism for protein folding. J. Mol. Biol. 254:260-288.
-
(1995)
J. Mol. Biol.
, vol.254
, pp. 260-288
-
-
Itzhaki, L.S.1
Otzen, D.E.2
Fersht, A.R.3
-
19
-
-
0036295960
-
Stiffness of the distal loop restricts the structural heterogeneity of the transition state ensemble in SH3 domains
-
Klimov, D. K., and D. Thirumalai. 2002. Stiffness of the distal loop restricts the structural heterogeneity of the transition state ensemble in SH3 domains. J. Mol. Biol. 315:721-737.
-
(2002)
J. Mol. Biol.
, vol.315
, pp. 721-737
-
-
Klimov, D.K.1
Thirumalai, D.2
-
20
-
-
0037195144
-
A simple physical model for binding energy hot spots in protein-protein complexes
-
Kortemme, T., and D. Baker. 2002. A simple physical model for binding energy hot spots in protein-protein complexes. Proc. Natl. Acad. Sci. USA. 99:14116-14121.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 14116-14121
-
-
Kortemme, T.1
Baker, D.2
-
21
-
-
0026244229
-
MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures
-
Kraulis, P. J. 1991. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallog. 24:946-950.
-
(1991)
J. Appl. Crystallog.
, vol.24
, pp. 946-950
-
-
Kraulis, P.J.1
-
22
-
-
0031465967
-
'New view' of protein folding reconciled with the old through multiple unfolding simulations
-
Lazaridis, T., and M. Karplus. 1997. 'New view' of protein folding reconciled with the old through multiple unfolding simulations. Science. 278:1928-1931.
-
(1997)
Science
, vol.278
, pp. 1928-1931
-
-
Lazaridis, T.1
Karplus, M.2
-
23
-
-
0028143603
-
Characterization of the transition state of protein unfolding by use of molecular dynamics: Chymotrypsin inhibitor 2
-
Li, A., and V. Daggett. 1994. Characterization of the transition state of protein unfolding by use of molecular dynamics: chymotrypsin inhibitor 2. Proc. Natl. Acad. Sci. USA. 91:10430-10434.
-
(1994)
Proc. Natl. Acad. Sci. USA
, vol.91
, pp. 10430-10434
-
-
Li, A.1
Daggett, V.2
-
24
-
-
0029963345
-
Identification and characterization of the unfolding transition state of chymotrypsin inhibitor 2 by molecular dynamics simulations
-
Li, A., and V. Daggett. 1996. Identification and characterization of the unfolding transition state of chymotrypsin inhibitor 2 by molecular dynamics simulations. J. Mol. Biol. 257:412-429.
-
(1996)
J. Mol. Biol.
, vol.257
, pp. 412-429
-
-
Li, A.1
Daggett, V.2
-
25
-
-
0035818481
-
Constructing, verifying, and dissecting the folding transition state of chymotrypsin inhibitor 2 with all-atom simulations
-
Li, L., and E. I. Shakhnovich. 2001. Constructing, verifying, and dissecting the folding transition state of chymotrypsin inhibitor 2 with all-atom simulations. Proc. Natl. Acad. Sci. USA. 98:13014-13018.
-
(2001)
Proc. Natl. Acad. Sci. USA
, vol.98
, pp. 13014-13018
-
-
Li, L.1
Shakhnovich, E.I.2
-
26
-
-
0024358426
-
Mapping the transition state and pathway of protein folding by protein engineering
-
Matouschek, A., J. T. J. Kellis, L. Serrano, and A. R. Fersht. 1989. Mapping the transition state and pathway of protein folding by protein engineering. Nature. 340:122-126.
-
(1989)
Nature
, vol.340
, pp. 122-126
-
-
Matouschek, A.1
Kellis, J.T.J.2
Serrano, L.3
Fersht, A.R.4
-
28
-
-
0036296248
-
Protein folding kinetics beyond the φ value: Using multiple amino acid substitutions to investigate the structure of the SH3 domain folding transition state
-
Northey, J. G., K. L. Maxwell, and A. R. Davidson. 2002a. Protein folding kinetics beyond the φ value: using multiple amino acid substitutions to investigate the structure of the SH3 domain folding transition state. J. Mol. Biol. 320:389-402.
-
(2002)
J. Mol. Biol.
, vol.320
, pp. 389-402
-
-
Northey, J.G.1
Maxwell, K.L.2
Davidson, A.R.3
-
29
-
-
0036172116
-
Hydrophobic core packing in the SH3 domain folding transition state
-
Northey, J. G., A. D. Nardo, and A. R. Davidson. 2002b. Hydrophobic core packing in the SH3 domain folding transition state. Nat. Struct. Biol. 9:126-130.
-
(2002)
Nat. Struct. Biol.
, vol.9
, pp. 126-130
-
-
Northey, J.G.1
Nardo, A.D.2
Davidson, A.R.3
-
30
-
-
0034681133
-
Landscape approaches to determine the ensemble of folding transition states: Success and failure hinge on the degree of frustration
-
Nymeyer, H., N. D. Socci, and J. N. Onuchic. 2000. Landscape approaches to determine the ensemble of folding transition states: success and failure hinge on the degree of frustration. Proc. Natl. Acad. Sci. USA. 97:634-639.
-
(2000)
Proc. Natl. Acad. Sci. USA
, vol.97
, pp. 634-639
-
-
Nymeyer, H.1
Socci, N.D.2
Onuchic, J.N.3
-
31
-
-
0036435907
-
Determination of a transition state at atomic resolution from protein engineering data
-
Paci, E., M. Vendruscolo, C. M. Dobson, and M. Karplus. 2002a. Determination of a transition state at atomic resolution from protein engineering data. J. Mol. Biol. 324:151-163.
-
(2002)
J. Mol. Biol.
, vol.324
, pp. 151-163
-
-
Paci, E.1
Vendruscolo, M.2
Dobson, C.M.3
Karplus, M.4
-
32
-
-
0036928148
-
Validity of Gō models: Comparison with a solvent-shielded empirical energy decomposition
-
Paci, E., M. Vendruscolo, and M. Karplus. 2002b. Validity of Gō models: Comparison with a solvent-shielded empirical energy decomposition. Biophys. J. 83:3032-3038.
-
(2002)
Biophys. J.
, vol.83
, pp. 3032-3038
-
-
Paci, E.1
Vendruscolo, M.2
Karplus, M.3
-
33
-
-
0035814880
-
Direct comparison of experimental and calculated folding free energies for hydrophobic deletion mutants of chymotrypsin inhibitor 2: Free energy perturbation calculations using transition and denatured states from molecular dynamics simulations of unfolding
-
Pan, Y., and V. Daggett. 2001. Direct comparison of experimental and calculated folding free energies for hydrophobic deletion mutants of chymotrypsin inhibitor 2: free energy perturbation calculations using transition and denatured states from molecular dynamics simulations of unfolding. Biochemistry. 40:2723-2731.
-
(2001)
Biochemistry
, vol.40
, pp. 2723-2731
-
-
Pan, Y.1
Daggett, V.2
-
34
-
-
0032734515
-
Experiment and theory highlight role of native state topology in SH3 folding
-
Riddle, D. S., V. P. Grantcharova, J. V. Santiago, E. Alm, I. Ruczinski, and D. Baker. 1999. Experiment and theory highlight role of native state topology in SH3 folding. Nat. Struct. Biol. 6:1016-1024.
-
(1999)
Nat. Struct. Biol.
, vol.6
, pp. 1016-1024
-
-
Riddle, D.S.1
Grantcharova, V.P.2
Santiago, J.V.3
Alm, E.4
Ruczinski, I.5
Baker, D.6
-
35
-
-
0034743155
-
From folding theories to folding proteins: A review and assessment of simulation studies of protein folding and unfolding
-
Shea, J.-E., and C. L. Brooks 3rd. 2001. From folding theories to folding proteins: a review and assessment of simulation studies of protein folding and unfolding. Annu. Rev. Phys. Chem. 52:499-535.
-
(2001)
Annu. Rev. Phys. Chem.
, vol.52
, pp. 499-535
-
-
Shea, J.-E.1
Brooks C.L. III2
-
36
-
-
0033515615
-
Exploring structures in protein folding funnels with free energy functionals: The transition state ensemble
-
Shoemaker, B. A., J. Wang, and P. G. Wolynes. 1999. Exploring structures in protein folding funnels with free energy functionals: the transition state ensemble. J. Mol. Biol. 287:675-694.
-
(1999)
J. Mol. Biol.
, vol.287
, pp. 675-694
-
-
Shoemaker, B.A.1
Wang, J.2
Wolynes, P.G.3
-
37
-
-
0036207492
-
Protein engineering study of protein L by simulation
-
Sorenson, J. M., and T. Head-Gordon. 2002. Protein engineering study of protein L by simulation. J. Comp. Biol. 9:35-54.
-
(2002)
J. Comp. Biol.
, vol.9
, pp. 35-54
-
-
Sorenson, J.M.1
Head-Gordon, T.2
-
38
-
-
0036836534
-
Non-native interactions, effective contact order, and protein folding: A mutational investigation with the energetically frustrated hydrophobic model
-
Treptow, W. L., M. A. A. Barbosa, L. G. Garcia, and A. F. P. de Araújo. 2002. Non-native interactions, effective contact order, and protein folding: a mutational investigation with the energetically frustrated hydrophobic model. Proteins. 49:167-180.
-
(2002)
Proteins.
, vol.49
, pp. 167-180
-
-
Treptow, W.L.1
Barbosa, M.A.A.2
Garcia, L.G.3
De Araújo, A.F.P.4
-
39
-
-
0345411345
-
Hierarchy of structure loss in MD simulations of src SH3 domain unfolding
-
Tsai, J., M. Levitt, and D. Baker. 1999. Hierarchy of structure loss in MD simulations of src SH3 domain unfolding. J. Mol. Biol. 291:215-225.
-
(1999)
J. Mol. Biol.
, vol.291
, pp. 215-225
-
-
Tsai, J.1
Levitt, M.2
Baker, D.3
-
40
-
-
0037311666
-
Protein folding: Bringing theory and experiments closer together
-
Vendruscolo, M., and E. Paci. 2003. Protein folding: bringing theory and experiments closer together. Curr. Op. Struct. Biol. 13:82-87.
-
(2003)
Curr. Op. Struct. Biol.
, vol.13
, pp. 82-87
-
-
Vendruscolo, M.1
Paci, E.2
-
41
-
-
0035252350
-
Three key residues form a critical contact network in protein folding transition state
-
Vendruscolo, M., E. Paci, C. M. Dobson, and M. Karplus. 2001. Three key residues form a critical contact network in protein folding transition state. Nature. 409:641-645.
-
(2001)
Nature
, vol.409
, pp. 641-645
-
-
Vendruscolo, M.1
Paci, E.2
Dobson, C.M.3
Karplus, M.4
-
42
-
-
0032515105
-
Structure of the transition state in the folding process of human procarboxypeptidase A2 activation domain
-
Villegas, V., J. C. Martinez, F. X. Avilés, and L. Serrano. 1998. Structure of the transition state in the folding process of human procarboxypeptidase A2 activation domain. J. Mol. Biol. 283:1027-1036.
-
(1998)
J. Mol. Biol.
, vol.283
, pp. 1027-1036
-
-
Villegas, V.1
Martinez, J.C.2
Avilés, F.X.3
Serrano, L.4
-
43
-
-
0025398721
-
WHAT-IF: A molecular modeling and drug design program
-
Vriend, G. 1990. WHAT-IF: a molecular modeling and drug design program. J. Mol. Graph. 8:52-56.
-
(1990)
J. Mol. Graph.
, vol.8
, pp. 52-56
-
-
Vriend, G.1
|