-
1
-
-
0028961335
-
SCOP: A structural classification of proteins database for the investigation of sequences and structures
-
A.G. Murzin SCOP: a structural classification of proteins database for the investigation of sequences and structures J. Mol. Biol. 247 1995 536 540
-
(1995)
J. Mol. Biol.
, vol.247
, pp. 536-540
-
-
Murzin, A.G.1
-
2
-
-
0029785147
-
Mapping the protein universe
-
L. Holm, and C. Sander Mapping the protein universe Science 273 1996 595 602
-
(1996)
Science
, vol.273
, pp. 595-602
-
-
Holm, L.1
Sander, C.2
-
3
-
-
0033977581
-
The ASTRAL compendium for protein structure and sequence analysis
-
S.E. Brenner The ASTRAL compendium for protein structure and sequence analysis Nucleic Acids Res. 28 2000 254 256
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 254-256
-
-
Brenner, S.E.1
-
4
-
-
0037418227
-
A global representation of the protein fold space
-
J. Hou A global representation of the protein fold space Proc. Natl. Acad. Sci. U. S. A. 100 2003 2386 2390
-
(2003)
Proc. Natl. Acad. Sci. U. S. A.
, vol.100
, pp. 2386-2390
-
-
Hou, J.1
-
5
-
-
0009586942
-
Understanding protein folding via free-energy surfaces from theory and experiment
-
A.R. Dinner Understanding protein folding via free-energy surfaces from theory and experiment Trends Biochem. Sci. 25 2000 331 339
-
(2000)
Trends Biochem. Sci.
, vol.25
, pp. 331-339
-
-
Dinner, A.R.1
-
6
-
-
0347357617
-
Protein folding and misfolding
-
C.M. Dobson Protein folding and misfolding Nature 426 2003 884 890
-
(2003)
Nature
, vol.426
, pp. 884-890
-
-
Dobson, C.M.1
-
7
-
-
0037221599
-
Is there a unifying mechanism for protein folding?
-
V. Daggett, and A.R. Fersht Is there a unifying mechanism for protein folding? Trends Biochem. Sci. 28 2003 18 25
-
(2003)
Trends Biochem. Sci.
, vol.28
, pp. 18-25
-
-
Daggett, V.1
Fersht, A.R.2
-
8
-
-
0035252350
-
Three key residues form a critical contact network in a protein folding transition state
-
M. Vendruscolo Three key residues form a critical contact network in a protein folding transition state Nature 409 2001 641 645
-
(2001)
Nature
, vol.409
, pp. 641-645
-
-
Vendruscolo, M.1
-
9
-
-
0035818481
-
Constructing, verifying, and dissecting the folding transition state of chymotrypsin inhibitor 2 with all-atom simulations
-
L. Li, and E.I. Shakhnovich Constructing, verifying, and dissecting the folding transition state of chymotrypsin inhibitor 2 with all-atom simulations Proc. Natl. Acad. Sci. U. S. A. 98 2001 13014 13018
-
(2001)
Proc. Natl. Acad. Sci. U. S. A.
, vol.98
, pp. 13014-13018
-
-
Li, L.1
Shakhnovich, E.I.2
-
10
-
-
0036435907
-
Determination of a transition state at atomic resolution from protein engineering data
-
E. Paci Determination of a transition state at atomic resolution from protein engineering data J. Mol. Biol. 324 2002 151 163
-
(2002)
J. Mol. Biol.
, vol.324
, pp. 151-163
-
-
Paci, E.1
-
11
-
-
0037457892
-
Self-consistent determination of the transition state for protein folding: Application to a fibronectin type III domain
-
E. Paci Self-consistent determination of the transition state for protein folding: application to a fibronectin type III domain Proc. Natl. Acad. Sci. U. S. A. 100 2003 394 399
-
(2003)
Proc. Natl. Acad. Sci. U. S. A.
, vol.100
, pp. 394-399
-
-
Paci, E.1
-
12
-
-
1042279571
-
Comparison of the transition states ensembles for folding of Im7 and Im9 determined using all-atom molecular dynamics simulations with Φ value restraints
-
E. Paci Comparison of the transition states ensembles for folding of Im7 and Im9 determined using all-atom molecular dynamics simulations with Φ value restraints Proteins 54 2004 513 525
-
(2004)
Proteins
, vol.54
, pp. 513-525
-
-
Paci, E.1
-
13
-
-
0842332830
-
Commitment and nucleation in the protein G transition state
-
I.A. Hubner Commitment and nucleation in the protein G transition state J. Mol. Biol. 336 2004 745 761
-
(2004)
J. Mol. Biol.
, vol.336
, pp. 745-761
-
-
Hubner, I.A.1
-
14
-
-
2942590388
-
Simulation, experiment, and evolution: Understanding nucleation in protein S6 folding
-
I.A. Hubner Simulation, experiment, and evolution: understanding nucleation in protein S6 folding Proc. Natl. Acad. Sci. U. S. A. 101 2004 8354 8359
-
(2004)
Proc. Natl. Acad. Sci. U. S. A.
, vol.101
, pp. 8354-8359
-
-
Hubner, I.A.1
-
15
-
-
2342451295
-
Transition states for protein folding have native topologies despite high structural variability
-
K. Lindorff-Larsen Transition states for protein folding have native topologies despite high structural variability Nat. Struct. Mol. Biol. 11 2004 443 449
-
(2004)
Nat. Struct. Mol. Biol.
, vol.11
, pp. 443-449
-
-
Lindorff-Larsen, K.1
-
16
-
-
0032502839
-
Contact order, transition state placement and the refolding rate of single domain proteins
-
K.W. Plaxco Contact order, transition state placement and the refolding rate of single domain proteins J. Mol. Biol. 277 1998 985 994
-
(1998)
J. Mol. Biol.
, vol.277
, pp. 985-994
-
-
Plaxco, K.W.1
-
17
-
-
0032980496
-
The topomer-sampling model of protein folding
-
D.A. Debe The topomer-sampling model of protein folding Proc. Natl. Acad. Sci. U. S. A. 96 1999 2596 2601
-
(1999)
Proc. Natl. Acad. Sci. U. S. A.
, vol.96
, pp. 2596-2601
-
-
Debe, D.A.1
-
18
-
-
0034604105
-
A surprising simplicity to protein folding
-
D. Baker A surprising simplicity to protein folding Nature 405 2000 39 42
-
(2000)
Nature
, vol.405
, pp. 39-42
-
-
Baker, D.1
-
19
-
-
0034687123
-
Topology, stability, sequence and length: Defining the determinants of two-state protein folding kinetics
-
K.W. Plaxco Topology, stability, sequence and length: Defining the determinants of two-state protein folding kinetics Biochemistry 39 2000 11177 11183
-
(2000)
Biochemistry
, vol.39
, pp. 11177-11183
-
-
Plaxco, K.W.1
-
20
-
-
0034652206
-
Transition-state structure as a unifying basis in protein-folding mechanisms: Contact order, chain topology, stability, and the extended nucleus mechanism
-
A.R. Fersht Transition-state structure as a unifying basis in protein-folding mechanisms: contact order, chain topology, stability, and the extended nucleus mechanism Proc. Natl. Acad. Sci. U. S. A. 97 2000 1525 1529
-
(2000)
Proc. Natl. Acad. Sci. U. S. A.
, vol.97
, pp. 1525-1529
-
-
Fersht, A.R.1
-
21
-
-
0037215268
-
The topomer search model: A simple, quantitative theory of two-state protein folding kinetics
-
D.E. Makarov, and K.W. Plaxco The topomer search model: a simple, quantitative theory of two-state protein folding kinetics Protein Sci. 12 2003 17 26
-
(2003)
Protein Sci.
, vol.12
, pp. 17-26
-
-
Makarov, D.E.1
Plaxco, K.W.2
-
22
-
-
3943113660
-
Using protein folding rates to test protein folding theories
-
B. Gillespie, and K.W. Plaxco Using protein folding rates to test protein folding theories Annu. Rev. Biochem. 73 2004 837 859
-
(2004)
Annu. Rev. Biochem.
, vol.73
, pp. 837-859
-
-
Gillespie, B.1
Plaxco, K.W.2
-
23
-
-
0031043161
-
Nucleation mechanisms in protein folding
-
A.R. Fersht Nucleation mechanisms in protein folding Curr. Opin. Struct. Biol. 7 1997 3 9
-
(1997)
Curr. Opin. Struct. Biol.
, vol.7
, pp. 3-9
-
-
Fersht, A.R.1
-
24
-
-
41349118690
-
Small-world view of the amino acids that play a key role in protein folding
-
M. Vendruscolo Small-world view of the amino acids that play a key role in protein folding Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 65 2002 061910
-
(2002)
Phys. Rev. e Stat. Nonlin. Soft Matter Phys.
, vol.65
, pp. 061910
-
-
Vendruscolo, M.1
-
25
-
-
0035029073
-
Protein structure: Geometry, topology and classification
-
W.R. Taylor Protein structure: geometry, topology and classification Rep. Prog. Phys. 64 2001 517 590
-
(2001)
Rep. Prog. Phys.
, vol.64
, pp. 517-590
-
-
Taylor, W.R.1
-
26
-
-
0037422619
-
Automatic classification of protein structure by using Gauss integrals
-
P. Røgen, and B. Fain Automatic classification of protein structure by using Gauss integrals Proc. Natl. Acad. Sci. U. S. A. 100 2003 119 124
-
(2003)
Proc. Natl. Acad. Sci. U. S. A.
, vol.100
, pp. 119-124
-
-
Røgen, P.1
Fain, B.2
-
27
-
-
0032708771
-
Mutational analysis of acylphosphatase suggests the importance of topology and contact order in protein folding
-
F. Chiti Mutational analysis of acylphosphatase suggests the importance of topology and contact order in protein folding Nat. Struct. Biol. 6 1999 1005 1009
-
(1999)
Nat. Struct. Biol.
, vol.6
, pp. 1005-1009
-
-
Chiti, F.1
-
28
-
-
0032750509
-
The folding transition state between SH3 domains is conformationally restricted and evolutionarily conserved
-
J.C. Martinez, and L. Serrano The folding transition state between SH3 domains is conformationally restricted and evolutionarily conserved Nat. Struct. Biol. 6 1999 1010 1016
-
(1999)
Nat. Struct. Biol.
, vol.6
, pp. 1010-1016
-
-
Martinez, J.C.1
Serrano, L.2
-
29
-
-
0034677663
-
The folding of an immunoglobulin-like greek key protein is defined by a common-core nucleus and regions constrained by topology
-
S.J. Hamill 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 2000 165 178
-
(2000)
J. Mol. Biol.
, vol.297
, pp. 165-178
-
-
Hamill, S.J.1
-
30
-
-
0027440362
-
Protein structure comparison by alignment of distance matrices
-
L. Holm, and C. Sander Protein structure comparison by alignment of distance matrices J. Mol. Biol. 233 1993 123 138
-
(1993)
J. Mol. Biol.
, vol.233
, pp. 123-138
-
-
Holm, L.1
Sander, C.2
-
31
-
-
0033824470
-
DaliLite workbench for protein structure comparison
-
L. Holm, and J. Park DaliLite workbench for protein structure comparison Bioinformatics 16 2000 566 567
-
(2000)
Bioinformatics
, vol.16
, pp. 566-567
-
-
Holm, L.1
Park, J.2
-
32
-
-
0036600746
-
Automatic detection of remote homology
-
S. Dietmann Automatic detection of remote homology Curr. Opin. Struct. Biol. 12 2002 362 367
-
(2002)
Curr. Opin. Struct. Biol.
, vol.12
, pp. 362-367
-
-
Dietmann, S.1
-
33
-
-
0034704229
-
A global geometric framework for nonlinear dimensionality reduction
-
J.B. Tenenbaum A global geometric framework for nonlinear dimensionality reduction Science 290 2000 2319 2323
-
(2000)
Science
, vol.290
, pp. 2319-2323
-
-
Tenenbaum, J.B.1
-
34
-
-
0034710671
-
A deeply knotted protein structure and how it might fold
-
W.R. Taylor A deeply knotted protein structure and how it might fold Nature 406 2000 916 919
-
(2000)
Nature
, vol.406
, pp. 916-919
-
-
Taylor, W.R.1
-
35
-
-
0343063933
-
Structure of proteins: Packing of α-helices and pleated sheets
-
C. Chothia Structure of proteins: packing of α-helices and pleated sheets Proc. Natl. Acad. Sci. U. S. A. 74 1977 4130 4134
-
(1977)
Proc. Natl. Acad. Sci. U. S. A.
, vol.74
, pp. 4130-4134
-
-
Chothia, C.1
-
36
-
-
0037154980
-
Protein folding and unfolding at atomic resolution
-
A.R. Fersht, and V. Daggett Protein folding and unfolding at atomic resolution Cell 108 2002 573 582
-
(2002)
Cell
, vol.108
, pp. 573-582
-
-
Fersht, A.R.1
Daggett, V.2
-
37
-
-
0037453348
-
A thermodynamic and kinetic analysis of the folding pathway of an SH3 domain entropically stabilised by a redesigned hydrophobic core
-
E.S. Cobos A thermodynamic and kinetic analysis of the folding pathway of an SH3 domain entropically stabilised by a redesigned hydrophobic core J. Mol. Biol. 328 2003 221 233
-
(2003)
J. Mol. Biol.
, vol.328
, pp. 221-233
-
-
Cobos, E.S.1
-
38
-
-
0037379184
-
Structural and kinetic characterization of the simplified SH3 domain FP1
-
Q. Yi Structural and kinetic characterization of the simplified SH3 domain FP1 Protein Sci. 12 2003 776 783
-
(2003)
Protein Sci.
, vol.12
, pp. 776-783
-
-
Yi, Q.1
-
39
-
-
0036266942
-
Conformational strain in the hydrophobic core and its implications for protein folding and design
-
S. Ventura Conformational strain in the hydrophobic core and its implications for protein folding and design Nat. Struct. Biol. 9 2002 485 493
-
(2002)
Nat. Struct. Biol.
, vol.9
, pp. 485-493
-
-
Ventura, S.1
-
40
-
-
0345306764
-
Design of a novel globular protein fold with atomic-level accuracy
-
B. Kuhlman Design of a novel globular protein fold with atomic-level accuracy Science 302 2003 1364 1368
-
(2003)
Science
, vol.302
, pp. 1364-1368
-
-
Kuhlman, B.1
-
41
-
-
1842635571
-
Characterization of the folding energy landscapes of computer generated proteins suggests high folding free energy barriers and cooperativity may be consequences of natural selection
-
M. Scalley, and D. Baker Characterization of the folding energy landscapes of computer generated proteins suggests high folding free energy barriers and cooperativity may be consequences of natural selection J. Mol. Biol. 338 2004 573 583
-
(2004)
J. Mol. Biol.
, vol.338
, pp. 573-583
-
-
Scalley, M.1
Baker, D.2
-
42
-
-
0345598912
-
Structures and relative free energies of partially folded states of proteins
-
M. Vendruscolo Structures and relative free energies of partially folded states of proteins Proc. Natl. Acad. Sci. U. S. A. 100 2003 14817 14821
-
(2003)
Proc. Natl. Acad. Sci. U. S. A.
, vol.100
, pp. 14817-14821
-
-
Vendruscolo, M.1
-
43
-
-
0030729838
-
An extensively modified version of MolScript that includes greatly enhanced coloring capabilities
-
R.M. Esnouf An extensively modified version of MolScript that includes greatly enhanced coloring capabilities J. Mol. Graph. Model. 15 1997 132 134
-
(1997)
J. Mol. Graph. Model.
, vol.15
, pp. 132-134
-
-
Esnouf, R.M.1
-
44
-
-
0036367763
-
Reweighted atomic densities to represent ensembles of NMR structures
-
C.D. Schwieters, and G.M. Clore Reweighted atomic densities to represent ensembles of NMR structures J. Biomol. NMR 23 2002 221 225
-
(2002)
J. Biomol. NMR
, vol.23
, pp. 221-225
-
-
Schwieters, C.D.1
Clore, G.M.2
-
45
-
-
1842414289
-
The SH3 domain of Eps8 exists as a novel intertwined dimer
-
K.V. Kishan The SH3 domain of Eps8 exists as a novel intertwined dimer Nat. Struct. Biol. 4 1997 739 743
-
(1997)
Nat. Struct. Biol.
, vol.4
, pp. 739-743
-
-
Kishan, K.V.1
-
46
-
-
0000171604
-
Differential geometry and polymer conformation 1. Comparison of protein conformations
-
S. Rackovsky, and H.A. Scheraga Differential geometry and polymer conformation 1. Comparison of protein conformations Macromolecules 11 1978 1168 1174
-
(1978)
Macromolecules
, vol.11
, pp. 1168-1174
-
-
Rackovsky, S.1
Scheraga, H.A.2
-
47
-
-
0242585484
-
A new family of global protein shape descriptors
-
P. Røgen, and H. Bohr A new family of global protein shape descriptors Math. Biosci. 182 2003 167 181
-
(2003)
Math. Biosci.
, vol.182
, pp. 167-181
-
-
Røgen, P.1
Bohr, H.2
|