-
1
-
-
0028963219
-
A test of lattice protein folding algorithms
-
Yue K, Fiebig KM, Thomas PD, Chan HS, Shakhnovich EI, et al. (1995) A test of lattice protein folding algorithms. Proc Natl Acad Sci U S A 92: 325-329.
-
(1995)
Proc Natl Acad Sci U S A
, vol.92
, pp. 325-329
-
-
Yue, K.1
Fiebig, K.M.2
Thomas, P.D.3
Chan, H.S.4
Shakhnovich, E.I.5
-
3
-
-
24944493938
-
Toward high-resolution de novo structure prediction for small proteins
-
Bradley P, Misura KMS, Baker D (2005) Toward high-resolution de novo structure prediction for small proteins. Science 309: 1868-1871.
-
(2005)
Science
, vol.309
, pp. 1868-1871
-
-
Bradley, P.1
Misura, K.M.S.2
Baker, D.3
-
4
-
-
33745024278
-
Symmetry, form, and shape: Guiding principles for robustness in macromolecular machines
-
Tama F, Brooks CL, III (2006) Symmetry, form, and shape: Guiding principles for robustness in macromolecular machines. Annu Rev Biophys Biomol Struct 35: 115-133.
-
(2006)
Annu Rev Biophys Biomol Struct
, vol.35
, pp. 115-133
-
-
Tama, F.1
Brooks III, C.L.2
-
5
-
-
0016696599
-
Studies on protein folding, unfolding and fluctuations by computer simulation. 1. Effect of specific amino acid sequence represented by specific inter-unit interactions
-
Taketomi H, Ueda Y, Go N (1975) Studies on protein folding, unfolding and fluctuations by computer simulation. 1. Effect of specific amino acid sequence represented by specific inter-unit interactions. Int J Pept Protein Res 7: 445-459.
-
(1975)
Int J Pept Protein Res
, vol.7
, pp. 445-459
-
-
Taketomi, H.1
Ueda, Y.2
Go, N.3
-
6
-
-
39149100599
-
Coarse-grained models of protein folding: Toy models or predictive tools?
-
Clementi C (2008) Coarse-grained models of protein folding: Toy models or predictive tools? Curr Opin Struct Biol 18: 10-15.
-
(2008)
Curr Opin Struct Biol
, vol.18
, pp. 10-15
-
-
Clementi, C.1
-
7
-
-
63449129633
-
Insights from coarse-grained Go models for protein folding and dynamics
-
Hills RD, Jr., Brooks CL, III (2009) Insights from coarse-grained Go models for protein folding and dynamics. Int J Mol Sci 10: 889-905.
-
(2009)
Int J Mol Sci
, vol.10
, pp. 889-905
-
-
Hills Jr., R.D.1
Brooks III, C.L.2
-
8
-
-
33644644163
-
Insertion and assembly of membrane proteins via simulation
-
Bond PJ, Sansom MSP (2006) Insertion and assembly of membrane proteins via simulation. J Am Chem Soc 128: 2697-2704.
-
(2006)
J Am Chem Soc
, vol.128
, pp. 2697-2704
-
-
Bond, P.J.1
Sansom, M.S.P.2
-
9
-
-
49449113010
-
The MARTINI coarse-grained force field: Extension to proteins
-
Monticelli L, Kandasamy SK, Periole X, Larson RG, Tieleman DP, et al. (2008) The MARTINI coarse-grained force field: Extension to proteins. J Chem Theory Comput 4: 819-834.
-
(2008)
J Chem Theory Comput
, vol.4
, pp. 819-834
-
-
Monticelli, L.1
Kandasamy, S.K.2
Periole, X.3
Larson, R.G.4
Tieleman, D.P.5
-
10
-
-
73349084983
-
Combining an elastic network with a coarse-grained molecular force field: Structure, dynamics, and intermolecular recognition
-
Periole X, Cavalli M, Marrink SJ, Ceruso MA (2009) Combining an elastic network with a coarse-grained molecular force field: Structure, dynamics, and intermolecular recognition. J Chem Theory Comput 5: 2531-2543.
-
(2009)
J Chem Theory Comput
, vol.5
, pp. 2531-2543
-
-
Periole, X.1
Cavalli, M.2
Marrink, S.J.3
Ceruso, M.A.4
-
11
-
-
33644893631
-
Coarse grained protein-lipid model with application to lipoprotein particles
-
Shih AY, Arkhipov A, Freddolino PL, Schulten K (2006) Coarse grained protein-lipid model with application to lipoprotein particles. J Phys Chem B 110: 3674-3684.
-
(2006)
J Phys Chem B
, vol.110
, pp. 3674-3684
-
-
Shih, A.Y.1
Arkhipov, A.2
Freddolino, P.L.3
Schulten, K.4
-
12
-
-
38549133951
-
A coarse-grained alpha-carbon protein model with anisotropic hydrogen-bonding
-
Yap EH, Fawzi NL, Head-Gordon T (2008) A coarse-grained alpha-carbon protein model with anisotropic hydrogen-bonding. Proteins 70: 626-638.
-
(2008)
Proteins
, vol.70
, pp. 626-638
-
-
Yap, E.H.1
Fawzi, N.L.2
Head-Gordon, T.3
-
13
-
-
70349458094
-
A force field for virtual atom molecular mechanics of proteins
-
Korkut A, Hendrickson WA (2009) A force field for virtual atom molecular mechanics of proteins. Proc Natl Acad Sci U S A 106: 15667-15672.
-
(2009)
Proc Natl Acad Sci U S A
, vol.106
, pp. 15667-15672
-
-
Korkut, A.1
Hendrickson, W.A.2
-
15
-
-
58149250463
-
Toward a coarse-grained protein model coupled with a coarse-grained solvent model: Solvation free energies of amino acid side chains
-
Han W, Wan CK, Wu YD (2008) Toward a coarse-grained protein model coupled with a coarse-grained solvent model: Solvation free energies of amino acid side chains. J Chem Theory Comput 4: 1891-1901.
-
(2008)
J Chem Theory Comput
, vol.4
, pp. 1891-1901
-
-
Han, W.1
Wan, C.K.2
Wu, Y.D.3
-
16
-
-
77950112700
-
A coarse-grained model based on morse potential for water and n-alkanes
-
Chiu SW, Scott HL, Jakobsson E (2010) A coarse-grained model based on morse potential for water and n-alkanes. J Chem Theory Comput 6: 851-863.
-
(2010)
J Chem Theory Comput
, vol.6
, pp. 851-863
-
-
Chiu, S.W.1
Scott, H.L.2
Jakobsson, E.3
-
17
-
-
34547474332
-
The MARTINI force field: Coarse grained model for biomolecular simulations
-
Marrink SJ, Risselada HJ, Yefimov S, Tieleman DP, de Vries AH (2007) The MARTINI force field: Coarse grained model for biomolecular simulations. J Phys Chem B 111: 7812-7824.
-
(2007)
J Phys Chem B
, vol.111
, pp. 7812-7824
-
-
Marrink, S.J.1
Risselada, H.J.2
Yefimov, S.3
Tieleman, D.P.4
de Vries, A.H.5
-
18
-
-
67649101377
-
Generic coarse-grained model for protein folding and aggregation
-
Bereau T, Deserno M (2009) Generic coarse-grained model for protein folding and aggregation. J Chem Phys 130: 235106.
-
(2009)
J Chem Phys
, vol.130
, pp. 235106
-
-
Bereau, T.1
Deserno, M.2
-
19
-
-
22544446147
-
Balancing energy and entropy: A minimalist model for the characterization of protein folding landscapes
-
Das P, Matysiak S, Clementi C (2005) Balancing energy and entropy: A minimalist model for the characterization of protein folding landscapes. Proc Natl Acad Sci U S A 102: 10141-10146.
-
(2005)
Proc Natl Acad Sci U S A
, vol.102
, pp. 10141-10146
-
-
Das, P.1
Matysiak, S.2
Clementi, C.3
-
20
-
-
34548809141
-
A coarse-grained protein force field for folding and structure prediction
-
Maupetit J, Tuffery P, Derreumaux P (2007) A coarse-grained protein force field for folding and structure prediction. Proteins 69: 394-408.
-
(2007)
Proteins
, vol.69
, pp. 394-408
-
-
Maupetit, J.1
Tuffery, P.2
Derreumaux, P.3
-
22
-
-
0032606941
-
Folding dynamics with nonadditive forces: A simulation study of a designed helical protein and a random heteropolymer
-
Takada S, Luthey-Schulten Z, Wolynes PG (1999) Folding dynamics with nonadditive forces: A simulation study of a designed helical protein and a random heteropolymer. J Chem Phys 110: 11616-11629.
-
(1999)
J Chem Phys
, vol.110
, pp. 11616-11629
-
-
Takada, S.1
Luthey-Schulten, Z.2
Wolynes, P.G.3
-
23
-
-
65949085330
-
Another look at the conditions for the extraction of protein knowledge-based potentials
-
Betancourt MR (2009) Another look at the conditions for the extraction of protein knowledge-based potentials. Proteins 76: 72-85.
-
(2009)
Proteins
, vol.76
, pp. 72-85
-
-
Betancourt, M.R.1
-
24
-
-
34548064535
-
Orientation-dependent potential of mean force for protein folding
-
Mukherjee A, Bhimalapuram P, Bagchi B (2005) Orientation-dependent potential of mean force for protein folding. J Chem Phys 123: 14901.
-
(2005)
J Chem Phys
, vol.123
, pp. 14901
-
-
Mukherjee, A.1
Bhimalapuram, P.2
Bagchi, B.3
-
25
-
-
68149165350
-
A coarse-grained potential for fold recognition and molecular dynamics simulations of proteins
-
Majek P, Elber R (2009) A coarse-grained potential for fold recognition and molecular dynamics simulations of proteins. Proteins 76: 822-836.
-
(2009)
Proteins
, vol.76
, pp. 822-836
-
-
Majek, P.1
Elber, R.2
-
26
-
-
34250829219
-
OPUS-Ca: A knowledge-based potential function requiring only C alpha positions
-
Wu YH, Lu MY, Chen MZ, Li JL, Ma JP (2007) OPUS-Ca: A knowledge-based potential function requiring only C alpha positions. Protein Sci 16: 1449-1463.
-
(2007)
Protein Sci
, vol.16
, pp. 1449-1463
-
-
Wu, Y.H.1
Lu, M.Y.2
Chen, M.Z.3
Li, J.L.4
Ma, J.P.5
-
27
-
-
1842861587
-
Development of novel statistical potentials for protein fold recognition
-
Buchete NV, Straub JE, Thirumalai D (2004) Development of novel statistical potentials for protein fold recognition. Curr Opin Struct Biol 14: 225-232.
-
(2004)
Curr Opin Struct Biol
, vol.14
, pp. 225-232
-
-
Buchete, N.V.1
Straub, J.E.2
Thirumalai, D.3
-
28
-
-
52349118400
-
Simple physics-based analytical formulas for the potentials of mean force for the interaction of amino acid side chains in water. IV. Pairs of different hydrophobic side chains
-
Makowski M, Sobolewski E, Czaplewski C, Oldziej S, Liwo A, et al. (2008) Simple physics-based analytical formulas for the potentials of mean force for the interaction of amino acid side chains in water. IV. Pairs of different hydrophobic side chains. J Phys Chem B 112: 11385-11395.
-
(2008)
J Phys Chem B
, vol.112
, pp. 11385-11395
-
-
Makowski, M.1
Sobolewski, E.2
Czaplewski, C.3
Oldziej, S.4
Liwo, A.5
-
29
-
-
69949126518
-
Exploring the parameter space of the coarse-grained UNRES force field by random search: Selecting a transferable medium-resolution force field
-
He Y, Xiao Y, Liwo A, Scheraga HA (2009) Exploring the parameter space of the coarse-grained UNRES force field by random search: Selecting a transferable medium-resolution force field. J Comput Chem 30: 2127-2135.
-
(2009)
J Comput Chem
, vol.30
, pp. 2127-2135
-
-
He, Y.1
Xiao, Y.2
Liwo, A.3
Scheraga, H.A.4
-
30
-
-
65949084921
-
Pairwise energies for polypeptide coarsegrained models derived from atomic force fields
-
Betancourt MR, Omovie SJ (2009) Pairwise energies for polypeptide coarsegrained models derived from atomic force fields. J Chem Phys 130: 195103.
-
(2009)
J Chem Phys
, vol.130
, pp. 195103
-
-
Betancourt, M.R.1
Omovie, S.J.2
-
31
-
-
34548020295
-
A coarse-grained protein-protein potential derived from an all-atom force field
-
Basdevant N, Borgis D, Ha-Duong T (2007) A coarse-grained protein-protein potential derived from an all-atom force field. J Phys Chem B 111: 9390-9399.
-
(2007)
J Phys Chem B
, vol.111
, pp. 9390-9399
-
-
Basdevant, N.1
Borgis, D.2
Ha-Duong, T.3
-
32
-
-
36649006847
-
Systematic coarse graining of biomolecular and soft-matter systems
-
Ayton GS, Noid WG, Voth GA (2007) Systematic coarse graining of biomolecular and soft-matter systems. MRS Bull 32: 929-934.
-
(2007)
MRS Bull
, vol.32
, pp. 929-934
-
-
Ayton, G.S.1
Noid, W.G.2
Voth, G.A.3
-
33
-
-
33644929350
-
Multiscale coarse graining of liquid-state systems
-
Izvekov S, Voth GA (2005) Multiscale coarse graining of liquid-state systems. J Chem Phys 123: 134105.
-
(2005)
J Chem Phys
, vol.123
, pp. 134105
-
-
Izvekov, S.1
Voth, G.A.2
-
34
-
-
14544291957
-
A multiscale coarse-graining method for biomolecular systems
-
Izvekov S, Voth GA (2005) A multiscale coarse-graining method for biomolecular systems. J Phys Chem B 109: 2469-2473.
-
(2005)
J Phys Chem B
, vol.109
, pp. 2469-2473
-
-
Izvekov, S.1
Voth, G.A.2
-
35
-
-
46149109506
-
The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models
-
Noid WG, Chu JW, Ayton GS, Krishna V, Izvekov S, et al. (2008) The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models. J Chem Phys 128: 244114.
-
(2008)
J Chem Phys
, vol.128
, pp. 244114
-
-
Noid, W.G.1
Chu, J.W.2
Ayton, G.S.3
Krishna, V.4
Izvekov, S.5
-
36
-
-
34248359980
-
Multiscale coarse-graining and structural correlations: Connections to liquid-state theory
-
Noid WG, Chu JW, Ayton GS, Voth GA (2007) Multiscale coarse-graining and structural correlations: Connections to liquid-state theory. J Phys Chem B 111: 4116-4127.
-
(2007)
J Phys Chem B
, vol.111
, pp. 4116-4127
-
-
Noid, W.G.1
Chu, J.W.2
Ayton, G.S.3
Voth, G.A.4
-
37
-
-
46149099398
-
The multiscale coarse-graining method. II. Numerical implementation for coarse-grained molecular models
-
Noid WG, Liu P, Wang Y, Chu JW, Ayton GS, et al. (2008) The multiscale coarse-graining method. II. Numerical implementation for coarse-grained molecular models. J Chem Phys 128: 244115.
-
(2008)
J Chem Phys
, vol.128
, pp. 244115
-
-
Noid, W.G.1
Liu, P.2
Wang, Y.3
Chu, J.W.4
Ayton, G.S.5
-
38
-
-
0042783950
-
Deriving effective mesoscale potentials from atomistic simulations
-
Reith D, Putz M, Muller-Plathe F (2003) Deriving effective mesoscale potentials from atomistic simulations. J Comput Chem 24: 1624-1636.
-
(2003)
J Comput Chem
, vol.24
, pp. 1624-1636
-
-
Reith, D.1
Putz, M.2
Muller-Plathe, F.3
-
39
-
-
33645078713
-
Calculation of effective interaction potentials from radial distribution functions: A reverse Monte Carlo approach
-
Lyubartsev A, Laaksonen A (1995) Calculation of effective interaction potentials from radial distribution functions: A reverse Monte Carlo approach. Phys Rev E 52: 3730-3737.
-
(1995)
Phys Rev E
, vol.52
, pp. 3730-3737
-
-
Lyubartsev, A.1
Laaksonen, A.2
-
40
-
-
62349124337
-
Multiscale modeling of emergent materials: Biological and soft matter
-
Murtola T, Bunker A, Vattulainen I, Deserno M, Karttunen M (2009) Multiscale modeling of emergent materials: Biological and soft matter. Phys Chem Chem Phys 11: 1869-1892.
-
(2009)
Phys Chem Chem Phys
, vol.11
, pp. 1869-1892
-
-
Murtola, T.1
Bunker, A.2
Vattulainen, I.3
Deserno, M.4
Karttunen, M.5
-
41
-
-
57349094411
-
A Bayesian statistics approach to multiscale coarse graining
-
Liu P, Shi Q, Daume H, Voth GA (2008) A Bayesian statistics approach to multiscale coarse graining. J Chem Phys 129: 214114.
-
(2008)
J Chem Phys
, vol.129
, pp. 214114
-
-
Liu, P.1
Shi, Q.2
Daume, H.3
Voth, G.A.4
-
42
-
-
55149087047
-
Peptide folding using multiscale coarsegrained models
-
Thorpe IF, Zhou J, Voth GA (2008) Peptide folding using multiscale coarsegrained models. J Phys Chem B 112: 13079-13090.
-
(2008)
J Phys Chem B
, vol.112
, pp. 13079-13090
-
-
Thorpe, I.F.1
Zhou, J.2
Voth, G.A.3
-
43
-
-
34247852583
-
Coarse-grained peptide modeling using a systematic multiscale approach
-
Zhou J, Thorpe IF, Izvekov S, Voth GA (2007) Coarse-grained peptide modeling using a systematic multiscale approach. Biophys J 92: 4289-4303.
-
(2007)
Biophys J
, vol.92
, pp. 4289-4303
-
-
Zhou, J.1
Thorpe, I.F.2
Izvekov, S.3
Voth, G.A.4
-
44
-
-
0001616080
-
Replica-exchange molecular dynamics method for protein folding
-
Sugita Y, Okamoto Y (1999) Replica-exchange molecular dynamics method for protein folding. Chem Phys Lett 314: 141-151.
-
(1999)
Chem Phys Lett
, vol.314
, pp. 141-151
-
-
Sugita, Y.1
Okamoto, Y.2
-
46
-
-
33846213672
-
Mapping all-atom models onto one-bead coarse-grained models: General properties and applications to a minimal polypeptide model
-
Tozzini V, Rocchia W, McCammon JA (2006) Mapping all-atom models onto one-bead coarse-grained models: General properties and applications to a minimal polypeptide model. J Chem Theory Comput 2: 667-673.
-
(2006)
J Chem Theory Comput
, vol.2
, pp. 667-673
-
-
Tozzini, V.1
Rocchia, W.2
McCammon, J.A.3
-
47
-
-
64749094483
-
Solvent-free lipid bilayer model using multiscale coarse-graining
-
Izvekov S, Voth GA (2009) Solvent-free lipid bilayer model using multiscale coarse-graining. J Phys Chem B 113: 4443-4455.
-
(2009)
J Phys Chem B
, vol.113
, pp. 4443-4455
-
-
Izvekov, S.1
Voth, G.A.2
-
48
-
-
61949390790
-
Systematic coarse-graining of a multicomponent lipid bilayer
-
Lu L, Voth GA (2009) Systematic coarse-graining of a multicomponent lipid bilayer. J Phys Chem B 113: 1501-1510.
-
(2009)
J Phys Chem B
, vol.113
, pp. 1501-1510
-
-
Lu, L.1
Voth, G.A.2
-
49
-
-
46249092554
-
GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation
-
Hess B, Kutzner C, van der Spoel D, Lindahl E (2008) GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation. J Chem Theory Comput 4: 435-447.
-
(2008)
J Chem Theory Comput
, vol.4
, pp. 435-447
-
-
Hess, B.1
Kutzner, C.2
van der Spoel, D.3
Lindahl, E.4
-
50
-
-
0036785556
-
The origins of asymmetry in the folding transition states of protein L and protein G
-
Karanicolas J, Brooks CL, III (2002) The origins of asymmetry in the folding transition states of protein L and protein G. Protein Sci 11: 2351-2361.
-
(2002)
Protein Sci
, vol.11
, pp. 2351-2361
-
-
Karanicolas, J.1
Brooks III, C.L.2
-
51
-
-
0035913529
-
Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides
-
Kaminski GA, Friesner RA, Tirado-Rives J, Jorgensen WL (2001) Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides. J Phys Chem B 105: 6474-6487.
-
(2001)
J Phys Chem B
, vol.105
, pp. 6474-6487
-
-
Kaminski, G.A.1
Friesner, R.A.2
Tirado-Rives, J.3
Jorgensen, W.L.4
-
52
-
-
61849107389
-
Temperature-transferable coarse-grained potentials for ethylbenzene, polystyrene, and their mixtures
-
Qian HJ, Carbone P, Chen X, Karimi-Varzaneh HA, Liew CC, et al. (2008) Temperature-transferable coarse-grained potentials for ethylbenzene, polystyrene, and their mixtures. Macromolecules 41: 9919-9929.
-
(2008)
Macromolecules
, vol.41
, pp. 9919-9929
-
-
Qian, H.J.1
Carbone, P.2
Chen, X.3
Karimi-Varzaneh, H.A.4
Liew, C.C.5
-
53
-
-
77951110879
-
A complete thermodynamic characterization of electrostatic and hydrophobic associations in the temperature range 0 to 100 C from explicit-solvent molecular dynamics simulations
-
Zhu S, Elcock AH (2010) A complete thermodynamic characterization of electrostatic and hydrophobic associations in the temperature range 0 to 100 C from explicit-solvent molecular dynamics simulations. J Chem Theory Comput 6: 1293-1306.
-
(2010)
J Chem Theory Comput
, vol.6
, pp. 1293-1306
-
-
Zhu, S.1
Elcock, A.H.2
-
56
-
-
77950149115
-
Efficient, regularized, and scalable algorithms for multiscale coarse-graining
-
Lu L, Izvekov S, Das A, Andersen HC, Voth GA (2010) Efficient, regularized, and scalable algorithms for multiscale coarse-graining. J Chem Theory Comput 6: 954-965.
-
(2010)
J Chem Theory Comput
, vol.6
, pp. 954-965
-
-
Lu, L.1
Izvekov, S.2
Das, A.3
Andersen, H.C.4
Voth, G.A.5
-
57
-
-
41549127613
-
A temperature predictor for parallel tempering simulations
-
Patriksson A, van der Spoel D (2008) A temperature predictor for parallel tempering simulations. Phys Chem Chem Phys 10: 2073-2077.
-
(2008)
Phys Chem Chem Phys
, vol.10
, pp. 2073-2077
-
-
Patriksson, A.1
van der Spoel, D.2
-
59
-
-
42049087036
-
Implicit modeling of nonpolar solvation for simulating protein folding and conformational transitions
-
Chen J, Brooks CL, III (2008) Implicit modeling of nonpolar solvation for simulating protein folding and conformational transitions. Phys Chem Chem Phys 10: 471-481.
-
(2008)
Phys Chem Chem Phys
, vol.10
, pp. 471-481
-
-
Chen, J.1
Brooks III, C.L.2
-
60
-
-
34247251976
-
Representability problems for coarse-grained water potentials
-
Johnson ME, Head-Gordon T, Louis AA (2007) Representability problems for coarse-grained water potentials. J Chem Phys 126: 144509.
-
(2007)
J Chem Phys
, vol.126
, pp. 144509
-
-
Johnson, M.E.1
Head-Gordon, T.2
Louis, A.A.3
-
61
-
-
62349089500
-
Self-assembling dipeptides: Conformational sampling in solvent-free coarse-grained simulation
-
Villa A, Peter C, van der Vegt NFA (2009) Self-assembling dipeptides: Conformational sampling in solvent-free coarse-grained simulation. Phys Chem Chem Phys 11: 2077-2086.
-
(2009)
Phys Chem Chem Phys
, vol.11
, pp. 2077-2086
-
-
Villa, A.1
Peter, C.2
van der Vegt, N.F.A.3
-
62
-
-
62349108293
-
Self-assembling dipeptides: Including solvent degrees of freedom in a coarse-grained model
-
Villa A, van der Vegt NFA, Peter C (2009) Self-assembling dipeptides: Including solvent degrees of freedom in a coarse-grained model. Phys Chem Chem Phys 11: 2068-2076.
-
(2009)
Phys Chem Chem Phys
, vol.11
, pp. 2068-2076
-
-
Villa, A.1
van der Vegt, N.F.A.2
Peter, C.3
-
63
-
-
36749008588
-
Large-scale allosteric conformational transitions of adenylate kinase appear to involve a population-shift mechanism
-
Arora K, Brooks CL, III (2007) Large-scale allosteric conformational transitions of adenylate kinase appear to involve a population-shift mechanism. Proc Natl Acad Sci U S A 104: 18496-18501.
-
(2007)
Proc Natl Acad Sci U S A
, vol.104
, pp. 18496-18501
-
-
Arora, K.1
Brooks III, C.L.2
-
64
-
-
64549108040
-
Noncooperative folding of subdomains in adenylate kinase
-
Rundqvist L, Aden J, Sparrman T, Wallgren M, Olsson U, et al. (2009) Noncooperative folding of subdomains in adenylate kinase. Biochemistry 48: 1911-1927.
-
(2009)
Biochemistry
, vol.48
, pp. 1911-1927
-
-
Rundqvist, L.1
Aden, J.2
Sparrman, T.3
Wallgren, M.4
Olsson, U.5
-
65
-
-
36849039429
-
A hierarchy of timescales in protein dynamics is linked to enzyme catalysis
-
Henzler-Wildman KA, Lei M, Thai V, Kerns SJ, Karplus M, et al. (2007) A hierarchy of timescales in protein dynamics is linked to enzyme catalysis. Nature 450: 913-916.
-
(2007)
Nature
, vol.450
, pp. 913-916
-
-
Henzler-Wildman, K.A.1
Lei, M.2
Thai, V.3
Kerns, S.J.4
Karplus, M.5
-
66
-
-
33846847773
-
Conformational transitions of adenylate kinase: Switching by cracking
-
Whitford PC, Miyashita O, Levy Y, Onuchic JN (2007) Conformational transitions of adenylate kinase: Switching by cracking. J Mol Biol 366: 1661-1671.
-
(2007)
J Mol Biol
, vol.366
, pp. 1661-1671
-
-
Whitford, P.C.1
Miyashita, O.2
Levy, Y.3
Onuchic, J.N.4
-
67
-
-
70349462451
-
Computation of conformational transitions in proteins by virtual atom molecular mechanics as validated in application to adenylate kinase
-
Korkut A, Hendrickson WA (2009) Computation of conformational transitions in proteins by virtual atom molecular mechanics as validated in application to adenylate kinase. Proc Natl Acad Sci U S A 106: 15673-15678.
-
(2009)
Proc Natl Acad Sci U S A
, vol.106
, pp. 15673-15678
-
-
Korkut, A.1
Hendrickson, W.A.2
-
68
-
-
77951212412
-
PRIMO/PRIMONA: A coarse-grained model for proteins and nucleic acids that preserves near atomistic accuracy
-
Gopal SM, Mukherjee S, Cheng YM, Feig M (2010) PRIMO/PRIMONA: A coarse-grained model for proteins and nucleic acids that preserves near atomistic accuracy. Proteins 78: 1266-1281.
-
(2010)
Proteins
, vol.78
, pp. 1266-1281
-
-
Gopal, S.M.1
Mukherjee, S.2
Cheng, Y.M.3
Feig, M.4
-
69
-
-
60849124513
-
Generalized ensemble methods for de novo structure prediction
-
Shmygelska A, Levitt M (2009) Generalized ensemble methods for de novo structure prediction. Proc Natl Acad Sci U S A 106: 1415-1420.
-
(2009)
Proc Natl Acad Sci U S A
, vol.106
, pp. 1415-1420
-
-
Shmygelska, A.1
Levitt, M.2
-
70
-
-
38549162210
-
Native atomic burials, supplemented by physically motivated hydrogen bond constraints, contain sufficient information to determine the tertiary structure of small globular proteins
-
de Araujo AFP, Gomes ALC, Bursztyn AA, Shakhnovich EI (2008) Native atomic burials, supplemented by physically motivated hydrogen bond constraints, contain sufficient information to determine the tertiary structure of small globular proteins. Proteins 70: 971-983.
-
(2008)
Proteins
, vol.70
, pp. 971-983
-
-
de Araujo, A.F.P.1
Gomes, A.L.C.2
Bursztyn, A.A.3
Shakhnovich, E.I.4
-
71
-
-
1542319916
-
Cooperativity principles in protein folding
-
Chan HS, Shimizu S, Kaya H (2004) Cooperativity principles in protein folding. Methods Enzymol 380: 350-379.
-
(2004)
Methods Enzymol
, vol.380
, pp. 350-379
-
-
Chan, H.S.1
Shimizu, S.2
Kaya, H.3
-
72
-
-
65649148275
-
Desolvation barrier effects are a likely contributor to the remarkable diversity in the folding rates of small proteins
-
Ferguson A, Liu ZR, Chan HS (2009) Desolvation barrier effects are a likely contributor to the remarkable diversity in the folding rates of small proteins. J Mol Biol 389: 619-636.
-
(2009)
J Mol Biol
, vol.389
, pp. 619-636
-
-
Ferguson, A.1
Liu, Z.R.2
Chan, H.S.3
-
73
-
-
34247639441
-
Folding free-energy landscape of villin headpiece subdomain from molecular dynamics simulations
-
Lei HX, Wu C, Liu HG, Duan Y (2007) Folding free-energy landscape of villin headpiece subdomain from molecular dynamics simulations. Proc Natl Acad Sci U S A 104: 4925-4930.
-
(2007)
Proc Natl Acad Sci U S A
, vol.104
, pp. 4925-4930
-
-
Lei, H.X.1
Wu, C.2
Liu, H.G.3
Duan, Y.4
-
74
-
-
67650354848
-
A free-energy approach for all-atom protein simulation
-
Verma A, Wenzel W (2009) A free-energy approach for all-atom protein simulation. Biophys J 96: 3483-3494.
-
(2009)
Biophys J
, vol.96
, pp. 3483-3494
-
-
Verma, A.1
Wenzel, W.2
-
76
-
-
67650230368
-
Folding simulations of Trp-cage mini protein in explicit solvent using biasing potential replica-exchange molecular dynamics simulations
-
Kannan S, Zacharias M (2009) Folding simulations of Trp-cage mini protein in explicit solvent using biasing potential replica-exchange molecular dynamics simulations. Proteins 76: 448-460.
-
(2009)
Proteins
, vol.76
, pp. 448-460
-
-
Kannan, S.1
Zacharias, M.2
-
77
-
-
67149138047
-
Energy landscape of the Trpzip2 peptide
-
Nymeyer H (2009) Energy landscape of the Trpzip2 peptide. J Phys Chem B 113: 8288-8295.
-
(2009)
J Phys Chem B
, vol.113
, pp. 8288-8295
-
-
Nymeyer, H.1
-
78
-
-
46749127364
-
Are current molecular dynamics force fields too helical?
-
Best RB, Buchete NV, Hummer G (2008) Are current molecular dynamics force fields too helical? Biophys J 95: L7-L9.
-
(2008)
Biophys J
, vol.95
-
-
Best, R.B.1
Buchete, N.V.2
Hummer, G.3
|