-
1
-
-
80055081145
-
How fast-folding proteins fold
-
Lindorff-Larsen K, Piana S, Dror RO, Shaw DE (2011) How fast-folding proteins fold. Science 334(6055):517-520.
-
(2011)
Science
, vol.334
, Issue.6055
, pp. 517-520
-
-
Lindorff-Larsen, K.1
Piana, S.2
Dror, R.O.3
Shaw, D.E.4
-
2
-
-
0242299185
-
TOUCHSTONE: A unified approach to protein structure prediction
-
Skolnick J, et al. (2003) TOUCHSTONE: A unified approach to protein structure prediction. Proteins 53(Suppl 6):469-479.
-
(2003)
Proteins
, vol.53
, pp. 469-479
-
-
Skolnick, J.1
-
3
-
-
20044391863
-
The protein folding problem: Global optimization of the force fields
-
Scheraga HA, et al. (2004) The protein folding problem: Global optimization of the force fields. Front Biosci 9:3296-3323.
-
(2004)
Front Biosci
, vol.9
, pp. 3296-3323
-
-
Scheraga, H.A.1
-
4
-
-
17044393884
-
Coarse-grained models for proteins
-
Tozzini V (2005) Coarse-grained models for proteins. Curr Opin Struct Biol 15(2):144-150.
-
(2005)
Curr Opin Struct Biol
, vol.15
, Issue.2
, pp. 144-150
-
-
Tozzini, V.1
-
5
-
-
55149087047
-
Peptide folding using multiscale coarse-grained models
-
Thorpe IF, Zhou J, Voth GA (2008) Peptide folding using multiscale coarse-grained models. J Phys Chem B 112(41):13079-13090.
-
(2008)
J Phys Chem B
, vol.112
, Issue.41
, pp. 13079-13090
-
-
Thorpe, I.F.1
Zhou, J.2
Voth, G.A.3
-
6
-
-
0027435091
-
Prediction of protein conformation on the basis of a search for compact structures: Test on avian pancreatic polypeptide
-
Liwo A, Pincus MR, Wawak RJ, Rackovsky S, Scheraga HA (1993) Prediction of protein conformation on the basis of a search for compact structures: Test on avian pancreatic polypeptide. Protein Sci 2(10):1715-1731.
-
(1993)
Protein Sci
, vol.2
, Issue.10
, pp. 1715-1731
-
-
Liwo, A.1
Pincus, M.R.2
Wawak, R.J.3
Rackovsky, S.4
Scheraga, H.A.5
-
7
-
-
0000095892
-
A united-residue force field for off-lattice protein-structure simulations. I. Functional forms and parameters of long-range side-chain interaction potentials from protein crystal data
-
Liwo A, et al. (1997) A united-residue force field for off-lattice protein-structure simulations. I. Functional forms and parameters of long-range side-chain interaction potentials from protein crystal data. J Comput Chem 18:849-873.
-
(1997)
J Comput Chem
, vol.18
, pp. 849-873
-
-
Liwo, A.1
-
8
-
-
0000095890
-
A united-residue force field for off-lattice protein-structure simulations. II: Parameterization of local interactions and determination of the weights of energy terms by Z-score optimization
-
Liwo A, et al. (1997) A united-residue force field for off-lattice protein-structure simulations. II: Parameterization of local interactions and determination of the weights of energy terms by Z-score optimization. J Comput Chem 18:874-887.
-
(1997)
J Comput Chem
, vol.18
, pp. 874-887
-
-
Liwo, A.1
-
9
-
-
0035424584
-
Cumulant-based expressions for the multibody terms for the correlation between local and electrostatic interactions in the united-residue force field
-
Liwo A, Czaplewski C, Pillardy J, Scheraga HA (2001) Cumulant-based expressions for the multibody terms for the correlation between local and electrostatic interactions in the united-residue force field. J Chem Phys 115:2323-2347.
-
(2001)
J Chem Phys
, vol.115
, pp. 2323-2347
-
-
Liwo, A.1
Czaplewski, C.2
Pillardy, J.3
Scheraga, H.A.4
-
10
-
-
3142681595
-
Parametrization of backbone-electrostatic and multibody contributions to the UNRES force field for protein-structure prediction from ab initio energy surfaces of model systems
-
Liwo A, Ołdziej S, Czaplewski C, Kozlowska U, Scheraga HA (2004) Parametrization of backbone-electrostatic and multibody contributions to the UNRES force field for protein-structure prediction from ab initio energy surfaces of model systems. J Phys Chem B 108:9421-9438.
-
(2004)
J Phys Chem B
, vol.108
, pp. 9421-9438
-
-
Liwo, A.1
Ołdziej, S.2
Czaplewski, C.3
Kozlowska, U.4
Scheraga, H.A.5
-
11
-
-
8344277888
-
Optimization of the UNRES force field by hierarchical design of the potential-energy landscape. 2. Off-lattice tests of the method with single proteins
-
Ołdziej S, Liwo A, Czaplewski C, Pillardy J, Scheraga HA (2004) Optimization of the UNRES force field by hierarchical design of the potential-energy landscape. 2. Off-lattice tests of the method with single proteins. J Phys Chem B 108:16934-16949.
-
(2004)
J Phys Chem B
, vol.108
, pp. 16934-16949
-
-
Ołdziej, S.1
Liwo, A.2
Czaplewski, C.3
Pillardy, J.4
Scheraga, H.A.5
-
12
-
-
8344262957
-
Optimization of the UNRES force field by hierarchical design of the potential-energy landscape. 3. Use of many proteins in optimization
-
Ołdziej S, et al. (2004) Optimization of the UNRES force field by hierarchical design of the potential-energy landscape. 3. Use of many proteins in optimization. J Phys Chem B 108:16950-16959.
-
(2004)
J Phys Chem B
, vol.108
, pp. 16950-16959
-
-
Ołdziej, S.1
-
13
-
-
33847123661
-
Modification and optimization of the united-residue (UNRES) potential energy function for canonical simulations. I. Temperature dependence of the effective energy function and tests of the optimization method with single training proteins
-
Liwo A, et al. (2007) Modification and optimization of the united-residue (UNRES) potential energy function for canonical simulations. I. Temperature dependence of the effective energy function and tests of the optimization method with single training proteins. J Phys Chem B 111(1):260-285.
-
(2007)
J Phys Chem B
, vol.111
, Issue.1
, pp. 260-285
-
-
Liwo, A.1
-
14
-
-
77950477912
-
Investigation of protein folding by coarse-grained molecular dynamics with the UNRES force field
-
Maisuradze GG, Senet P, Czaplewski C, Liwo A, Scheraga HA (2010) Investigation of protein folding by coarse-grained molecular dynamics with the UNRES force field. J Phys Chem A 114(13):4471-4485.
-
(2010)
J Phys Chem A
, vol.114
, Issue.13
, pp. 4471-4485
-
-
Maisuradze, G.G.1
Senet, P.2
Czaplewski, C.3
Liwo, A.4
Scheraga, H.A.5
-
15
-
-
0001071357
-
Tuning the free-energy landscape of a WW domain by temperature, mutation, and truncation
-
Nguyen H, Jager M, Moretto A, Gruebele M, Kelly JW (2003) Tuning the free-energy landscape of a WW domain by temperature, mutation, and truncation. Proc Natl Acad Sci USA 100(7):3948-3953.
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, Issue.7
, pp. 3948-3953
-
-
Nguyen, H.1
Jager, M.2
Moretto, A.3
Gruebele, M.4
Kelly, J.W.5
-
16
-
-
0034061258
-
Structural analysis of WW domains and design of a WW prototype
-
Macias MJ, Gervais V, Civera C, Oschkinat H (2000) Structural analysis of WW domains and design of a WW prototype. Nat Struct Biol 7(5):375-379.
-
(2000)
Nat Struct Biol
, vol.7
, Issue.5
, pp. 375-379
-
-
Macias, M.J.1
Gervais, V.2
Civera, C.3
Oschkinat, H.4
-
17
-
-
0034704216
-
NeW wrinkles for an old domain
-
Sudol M, Hunter T (2000) NeW wrinkles for an old domain. Cell 103(7):1001-1004.
-
(2000)
Cell
, vol.103
, Issue.7
, pp. 1001-1004
-
-
Sudol, M.1
Hunter, T.2
-
18
-
-
0037386699
-
The structural basis for biphasic kinetics in the folding of the WW domain from a formin-binding protein: Lessons for protein design?
-
Karanicolas J, Brooks CL, 3rd (2003) The structural basis for biphasic kinetics in the folding of the WW domain from a formin-binding protein: Lessons for protein design? Proc Natl Acad Sci USA 100(7):3954-3959.
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, Issue.7
, pp. 3954-3959
-
-
Karanicolas, J.1
Brooks, C.L.2
-
19
-
-
14044266389
-
Ab initio simulations of protein-folding pathways by molecular dynamics with the united-residue model of polypeptide chains
-
Liwo A, Khalili M, Scheraga HA (2005) Ab initio simulations of protein-folding pathways by molecular dynamics with the united-residue model of polypeptide chains. Proc Natl Acad Sci USA 102(7):2362-2367.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, Issue.7
, pp. 2362-2367
-
-
Liwo, A.1
Khalili, M.2
Scheraga, H.A.3
-
20
-
-
33744927646
-
Folding, misfolding, and amyloid protofibril formation of WW domain FBP28
-
Mu Y, Nordenskiöld L, Tam JP (2006) Folding, misfolding, and amyloid protofibril formation of WW domain FBP28. Biophys J 90(11):3983-3992.
-
(2006)
Biophys J
, vol.90
, Issue.11
, pp. 3983-3992
-
-
Mu, Y.1
Nordenskiöld, L.2
Tam, J.P.3
-
21
-
-
57749191492
-
Principal component analysis for protein folding dynamics
-
Maisuradze GG, Liwo A, Scheraga HA (2009) Principal component analysis for protein folding dynamics. J Mol Biol 385(1):312-329.
-
(2009)
J Mol Biol
, vol.385
, Issue.1
, pp. 312-329
-
-
Maisuradze, G.G.1
Liwo, A.2
Scheraga, H.A.3
-
22
-
-
77950108200
-
Relation between free energy landscapes of proteins and dynamics
-
Maisuradze GG, Liwo A, Scheraga HA (2010) Relation between free energy landscapes of proteins and dynamics. J Chem Theory Comput 6(2):583-595.
-
(2010)
J Chem Theory Comput
, vol.6
, Issue.2
, pp. 583-595
-
-
Maisuradze, G.G.1
Liwo, A.2
Scheraga, H.A.3
-
23
-
-
77957937199
-
Atomic-level characterization of the structural dynamics of proteins
-
Shaw DE, et al. (2010) Atomic-level characterization of the structural dynamics of proteins. Science 330(6002):341-346.
-
(2010)
Science
, vol.330
, Issue.6002
, pp. 341-346
-
-
Shaw, D.E.1
-
24
-
-
78650415889
-
Computational design and experimental testing of the fastest-folding β-sheet protein
-
Piana S, et al. (2011) Computational design and experimental testing of the fastest-folding β-sheet protein. J Mol Biol 405(1):43-48.
-
(2011)
J Mol Biol
, vol.405
, Issue.1
, pp. 43-48
-
-
Piana, S.1
-
25
-
-
79955714681
-
The ensemble folding kinetics of the FBP28 WW domain revealed by an all-atom Monte Carlo simulation in a knowledge-based potential
-
Xu J, Huang L, Shakhnovich EI (2011) The ensemble folding kinetics of the FBP28 WW domain revealed by an all-atom Monte Carlo simulation in a knowledge-based potential. Proteins 79(6):1704-1714.
-
(2011)
Proteins
, vol.79
, Issue.6
, pp. 1704-1714
-
-
Xu, J.1
Huang, L.2
Shakhnovich, E.I.3
-
26
-
-
84857134132
-
Dominant folding pathways of a WW domain
-
A Beccara S, Škrbić T, Covino R, Faccioli P (2012) Dominant folding pathways of a WW domain. Proc Natl Acad Sci USA 109(7):2330-2335.
-
(2012)
Proc Natl Acad Sci USA
, vol.109
, Issue.7
, pp. 2330-2335
-
-
Beccara S, A.1
Škrbić, T.2
Covino, R.3
Faccioli, P.4
-
27
-
-
84862195114
-
Effects ofmutation, truncation, and temperature on the folding kinetics of a WW domain
-
Maisuradze GG, Zhou R, Liwo A, Xiao Y, Scheraga HA (2012) Effects ofmutation, truncation, and temperature on the folding kinetics of a WW domain. J Mol Biol 420(4-5):350-365.
-
(2012)
J Mol Biol
, vol.420
, Issue.4-5
, pp. 350-365
-
-
Maisuradze, G.G.1
Zhou, R.2
Liwo, A.3
Xiao, Y.4
Scheraga, H.A.5
-
28
-
-
84880014653
-
Local vs global motions in protein folding
-
Maisuradze GG, Liwo A, Senet P, Scheraga HA (2013) Local vs global motions in protein folding. J Chem Theory Comput 9(7):2907-2921.
-
(2013)
J Chem Theory Comput
, vol.9
, Issue.7
, pp. 2907-2921
-
-
Maisuradze, G.G.1
Liwo, A.2
Senet, P.3
Scheraga, H.A.4
-
29
-
-
0035839050
-
The folding mechanism of a beta-sheet: The WW domain
-
Jäger M, Nguyen H, Crane JC, Kelly JW, Gruebele M (2001) The folding mechanism of a beta-sheet: The WW domain. J Mol Biol 311(2):373-393.
-
(2001)
J Mol Biol
, vol.311
, Issue.2
, pp. 373-393
-
-
Jäger, M.1
Nguyen, H.2
Crane, J.C.3
Kelly, J.W.4
Gruebele, M.5
-
30
-
-
0035818471
-
Ultrafast folding of WW domains without structured aromatic clusters in the denatured state
-
Ferguson N, Johnson CM, Macias M, Oschkinat H, Fersht A (2001) Ultrafast folding of WW domains without structured aromatic clusters in the denatured state. Proc Natl Acad Sci USA 98(23):13002-13007.
-
(2001)
Proc Natl Acad Sci USA
, vol.98
, Issue.23
, pp. 13002-13007
-
-
Ferguson, N.1
Johnson, C.M.2
Macias, M.3
Oschkinat, H.4
Fersht, A.5
-
31
-
-
0043194015
-
Rapid amyloid fiber formation from the fast-folding WW domain FBP28
-
Ferguson N, et al. (2003) Rapid amyloid fiber formation from the fast-folding WW domain FBP28. Proc Natl Acad Sci USA 100(17):9814-9819.
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, Issue.17
, pp. 9814-9819
-
-
Ferguson, N.1
-
32
-
-
33745606942
-
Phi-analysis at the experimental limits: Mechanism of beta-hairpin formation
-
Petrovich M, Jonsson AL, Ferguson N, Daggett V, Fersht AR (2006) Phi-analysis at the experimental limits: Mechanism of beta-hairpin formation. J Mol Biol 360(4):865-881.
-
(2006)
J Mol Biol
, vol.360
, Issue.4
, pp. 865-881
-
-
Petrovich, M.1
Jonsson, A.L.2
Ferguson, N.3
Daggett, V.4
Fersht, A.R.5
-
33
-
-
33746042979
-
Structure-function-folding relationship in a WW domain
-
Jäger M, et al. (2006) Structure-function-folding relationship in a WW domain. Proc Natl Acad Sci USA 103(28):10648-10653.
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, Issue.28
, pp. 10648-10653
-
-
Jäger, M.1
-
34
-
-
34748919075
-
The role of the turn in beta-hairpin formation during WW domain folding
-
Sharpe T, Jonsson AL, Rutherford TJ, Daggett V, Fersht AR (2007) The role of the turn in beta-hairpin formation during WW domain folding. Protein Sci 16(10):2233-2239.
-
(2007)
Protein Sci
, vol.16
, Issue.10
, pp. 2233-2239
-
-
Sharpe, T.1
Jonsson, A.L.2
Rutherford, T.J.3
Daggett, V.4
Fersht, A.R.5
-
35
-
-
0034718157
-
Alzheimer's amyloid fibrils: Structure and assembly
-
Serpell LC (2000) Alzheimer's amyloid fibrils: Structure and assembly. Biochim Biophys Acta 1502(1):16-30.
-
(2000)
Biochim Biophys Acta
, vol.1502
, Issue.1
, pp. 16-30
-
-
Serpell, L.C.1
-
36
-
-
84906859873
-
WW domain folding complexity revealed by infrared spectroscopy
-
Davis CM, Dyer RB (2014) WW domain folding complexity revealed by infrared spectroscopy. Biochemistry 53(34):5476-5484.
-
(2014)
Biochemistry
, vol.53
, Issue.34
, pp. 5476-5484
-
-
Davis, C.M.1
Dyer, R.B.2
-
37
-
-
34547507851
-
Effects of crowding and confinement on the structures of the transition state ensemble in proteins
-
Cheung MS, Thirumalai D (2007) Effects of crowding and confinement on the structures of the transition state ensemble in proteins. J Phys Chem B 111(28):8250-8257.
-
(2007)
J Phys Chem B
, vol.111
, Issue.28
, pp. 8250-8257
-
-
Cheung, M.S.1
Thirumalai, D.2
-
38
-
-
0000050196
-
From minimal models to real proteins: Time scales for protein folding kinetics
-
Thirumalai D (1995) From minimal models to real proteins: Time scales for protein folding kinetics. J Phys I 5:1457-1467.
-
(1995)
J Phys I
, vol.5
, pp. 1457-1467
-
-
Thirumalai, D.1
-
39
-
-
84860013075
-
Structure of an intermediate state in protein folding and aggregation
-
Neudecker P, et al. (2012) Structure of an intermediate state in protein folding and aggregation. Science 336(6079):362-366.
-
(2012)
Science
, vol.336
, Issue.6079
, pp. 362-366
-
-
Neudecker, P.1
-
40
-
-
0030624384
-
Protein folding kinetics: Timescales, pathways and energy landscapes in terms of sequence-dependent properties
-
Veitshans T, Klimov D, Thirumalai D (1997) Protein folding kinetics: Timescales, pathways and energy landscapes in terms of sequence-dependent properties. Fold Des 2(1):1-22.
-
(1997)
Fold des
, vol.2
, Issue.1
, pp. 1-22
-
-
Veitshans, T.1
Klimov, D.2
Thirumalai, D.3
-
41
-
-
0036783392
-
Thermal folding and mechanical unfolding pathways of protein secondary structures
-
Cieplak M, Hoang TX, Robbins MO (2002) Thermal folding and mechanical unfolding pathways of protein secondary structures. Proteins 49(1):104-113.
-
(2002)
Proteins
, vol.49
, Issue.1
, pp. 104-113
-
-
Cieplak, M.1
Hoang, T.X.2
Robbins, M.O.3
|