-
1
-
-
0036280741
-
Molecular dynamics applied to X-ray structure refinement
-
Brunger A.T., and Adams P.D. Molecular dynamics applied to X-ray structure refinement. ACC. Chem. Res. 35 (2002) 404-412
-
(2002)
ACC. Chem. Res.
, vol.35
, pp. 404-412
-
-
Brunger, A.T.1
Adams, P.D.2
-
3
-
-
25844459462
-
-
University of California, San Francisco
-
Case D., Pearlman D.A., Caldwell J.W., Cheatham III T.E., Ross W.S., Simmerling C.L., Darden T.A., Merz K.M., Stanton R.V., Cheng A.L., Vincent J.J., Crowley M., Tsui V., Radmer R.J., Duan Y., Pitera J., Massova I., Seibel G.L., Singh U.C., Weiner P.K., and Kollman P.A. Amber 8 (2003), University of California, San Francisco
-
(2003)
Amber 8
-
-
Case, D.1
Pearlman, D.A.2
Caldwell, J.W.3
Cheatham III, T.E.4
Ross, W.S.5
Simmerling, C.L.6
Darden, T.A.7
Merz, K.M.8
Stanton, R.V.9
Cheng, A.L.10
Vincent, J.J.11
Crowley, M.12
Tsui, V.13
Radmer, R.J.14
Duan, Y.15
Pitera, J.16
Massova, I.17
Seibel, G.L.18
Singh, U.C.19
Weiner, P.K.20
Kollman, P.A.21
more..
-
4
-
-
0242663237
-
Point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations
-
Duan Y., Wu A., Chowdhury C.S., Lee M.C., Xiong G., Zhang W., Yang R., Cieplak P., Luo R., Lee T., Caldwell J., Wang J., and Kollman P.A. Point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. J. Comput. Chem. 24 (2003) 1999-2012
-
(2003)
J. Comput. Chem.
, vol.24
, pp. 1999-2012
-
-
Duan, Y.1
Wu, A.2
Chowdhury, C.S.3
Lee, M.C.4
Xiong, G.5
Zhang, W.6
Yang, R.7
Cieplak, P.8
Luo, R.9
Lee, T.10
Caldwell, J.11
Wang, J.12
Kollman, P.A.13
-
5
-
-
0037157317
-
On the Hamiltonian replica exchange method for efficient sampling of biomolecular systems: application to protein structure prediction
-
Fukunishi H., Watanabe O., and Takada S. On the Hamiltonian replica exchange method for efficient sampling of biomolecular systems: application to protein structure prediction. J. Chem. Phys. 116 (2002) 9058-9067
-
(2002)
J. Chem. Phys.
, vol.116
, pp. 9058-9067
-
-
Fukunishi, H.1
Watanabe, O.2
Takada, S.3
-
7
-
-
33646002994
-
Comparative modeling for protein structure prediction
-
Ginalski K. Comparative modeling for protein structure prediction. Curr. Opin. Struct. Biol. 16 (2006) 172-177
-
(2006)
Curr. Opin. Struct. Biol.
, vol.16
, pp. 172-177
-
-
Ginalski, K.1
-
8
-
-
0035008585
-
Energy landscape of a peptide consisting of alpha-helix, 3(10)-helix, beta-turn, beta-hairpin, and other disordered conformations
-
Higo J., Ito N., Kuroda M., Ono S., Nakajima N., and Nakamura H. Energy landscape of a peptide consisting of alpha-helix, 3(10)-helix, beta-turn, beta-hairpin, and other disordered conformations. Protein Sci. 10 (2001) 1160-1171
-
(2001)
Protein Sci.
, vol.10
, pp. 1160-1171
-
-
Higo, J.1
Ito, N.2
Kuroda, M.3
Ono, S.4
Nakajima, N.5
Nakamura, H.6
-
9
-
-
0025004291
-
Crystal structure of alpha 1: implications for protein design
-
Hill C.P., Anderson D.H., Wesson L., DeGrado W.F., and Eisenberg D. Crystal structure of alpha 1: implications for protein design. Science 249 (1990) 543-546
-
(1990)
Science
, vol.249
, pp. 543-546
-
-
Hill, C.P.1
Anderson, D.H.2
Wesson, L.3
DeGrado, W.F.4
Eisenberg, D.5
-
10
-
-
4143145167
-
10 residue folded peptide designed by segment statistics
-
Honda S., Yamasaki K., Sawada Y., and Morii H. 10 residue folded peptide designed by segment statistics. Structure 12 (2004) 1507-1518
-
(2004)
Structure
, vol.12
, pp. 1507-1518
-
-
Honda, S.1
Yamasaki, K.2
Sawada, Y.3
Morii, H.4
-
11
-
-
1242338103
-
Conformational sampling for the impatient
-
Kaihsu T. Conformational sampling for the impatient. Biophys. Chem. 107 (2004) 213-220
-
(2004)
Biophys. Chem.
, vol.107
, pp. 213-220
-
-
Kaihsu, T.1
-
12
-
-
36049031922
-
Folding of a DNA hairpin loop structure in explicit solvent using replica-exchange molecular dynamics simulations
-
Kannan S., and Zacharias M. Folding of a DNA hairpin loop structure in explicit solvent using replica-exchange molecular dynamics simulations. Biophys. J. 93 (2007) 3218-3228
-
(2007)
Biophys. J.
, vol.93
, pp. 3218-3228
-
-
Kannan, S.1
Zacharias, M.2
-
13
-
-
33846227108
-
Enhanced sampling of peptide and protein conformations using replica exchange simulations with a peptide backbone biasing-potential
-
Kannan S., and Zacharias M. Enhanced sampling of peptide and protein conformations using replica exchange simulations with a peptide backbone biasing-potential. Proteins 66 (2007) 697-706
-
(2007)
Proteins
, vol.66
, pp. 697-706
-
-
Kannan, S.1
Zacharias, M.2
-
15
-
-
0003533473
-
-
Larrhoven P.J.M., and Aarts E.H.L. (Eds), Reidel, Dordrecht pp. 187
-
In: Larrhoven P.J.M., and Aarts E.H.L. (Eds). Simulated Annealing: Theory and Applications (1987), Reidel, Dordrecht pp. 187
-
(1987)
Simulated Annealing: Theory and Applications
-
-
-
16
-
-
0030956593
-
Homology modeling using simulated annealing of restrained molecular dynamics and conformational search calculations with CONGEN: application in predicting the three-dimensional structure of murine homeodomain Msx-1
-
Li H., Tejero R., Monleon D., Bassolino-Klimas D., Abate-Shen C., Bruccoleri R.E., and Montelione G.T. Homology modeling using simulated annealing of restrained molecular dynamics and conformational search calculations with CONGEN: application in predicting the three-dimensional structure of murine homeodomain Msx-1. Protein Sci. 6 (1997) 956-970
-
(1997)
Protein Sci.
, vol.6
, pp. 956-970
-
-
Li, H.1
Tejero, R.2
Monleon, D.3
Bassolino-Klimas, D.4
Abate-Shen, C.5
Bruccoleri, R.E.6
Montelione, G.T.7
-
17
-
-
0000855275
-
Replica-exchange simulated tempering method for simulations of frustrated systems
-
Mitsutake A., and Okamoto Y. Replica-exchange simulated tempering method for simulations of frustrated systems. Chem. Phys. Lett. 332 (2000) 131-138
-
(2000)
Chem. Phys. Lett.
, vol.332
, pp. 131-138
-
-
Mitsutake, A.1
Okamoto, Y.2
-
18
-
-
0034864528
-
Generalized-ensemble algorithms for molecular simulations of biopolymers
-
Mitsutake A., Sugita Y., and Okamoto Y. Generalized-ensemble algorithms for molecular simulations of biopolymers. Biopolymers 60 (2001) 96-123
-
(2001)
Biopolymers
, vol.60
, pp. 96-123
-
-
Mitsutake, A.1
Sugita, Y.2
Okamoto, Y.3
-
19
-
-
4344612164
-
Replica-exchange extensions of simulated tempering method
-
Mitsutake A., and Okamoto Y. Replica-exchange extensions of simulated tempering method. J. Chem. Phys. 121 (2004) 2491-2504
-
(2004)
J. Chem. Phys.
, vol.121
, pp. 2491-2504
-
-
Mitsutake, A.1
Okamoto, Y.2
-
20
-
-
25444446805
-
A restraint molecular dynamics and simulated annealing approach for protein homology modeling utilizing mean angles
-
Möglich A., Weinfurtner D., Maurer T., Gronwald W., and Kalbitzer H.R. A restraint molecular dynamics and simulated annealing approach for protein homology modeling utilizing mean angles. BMC-Bioinformatics 6 (2005) 91
-
(2005)
BMC-Bioinformatics
, vol.6
, pp. 91
-
-
Möglich, A.1
Weinfurtner, D.2
Maurer, T.3
Gronwald, W.4
Kalbitzer, H.R.5
-
21
-
-
0344702698
-
Simulation of the folding equilibrium of α-helical peptides: a comparison of the generalized Born approximation with explicit solvent
-
Nymeyer H., and Garcia A.E. Simulation of the folding equilibrium of α-helical peptides: a comparison of the generalized Born approximation with explicit solvent. Proc. Natl. Acad. Sci. USA 100 (2003) 13934-13939
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 13934-13939
-
-
Nymeyer, H.1
Garcia, A.E.2
-
22
-
-
0028964702
-
Comparison of the free and DNA-complexed forms of the DNA-binding domain from c-Myb
-
Ogata K., Morikawa S., Nakamura H., Hojo H., Yoshimura S., Zhang R., Aimoto S., Ametani Y., Hirata Z., Sarai A., et al. Comparison of the free and DNA-complexed forms of the DNA-binding domain from c-Myb. Nat. Struct. Biol. 4 (1995) 309-320
-
(1995)
Nat. Struct. Biol.
, vol.4
, pp. 309-320
-
-
Ogata, K.1
Morikawa, S.2
Nakamura, H.3
Hojo, H.4
Yoshimura, S.5
Zhang, R.6
Aimoto, S.7
Ametani, Y.8
Hirata, Z.9
Sarai, A.10
-
23
-
-
0000551750
-
Replica-exchange Monte Carlo method for the isobaric-isothermal ensemble
-
Okabe T., Kawata M., Okamoto Y., and Mikami M. Replica-exchange Monte Carlo method for the isobaric-isothermal ensemble. Chem. Phys. Lett. 335 (2001) 435-439
-
(2001)
Chem. Phys. Lett.
, vol.335
, pp. 435-439
-
-
Okabe, T.1
Kawata, M.2
Okamoto, Y.3
Mikami, M.4
-
24
-
-
1942455272
-
Generalized-ensemble algorithms: enhanced sampling techniques for Monte Carlo and molecular dynamics simulations
-
Okamoto Y. Generalized-ensemble algorithms: enhanced sampling techniques for Monte Carlo and molecular dynamics simulations. J. Mol. Graph. Model. 22 (2004) 425-439
-
(2004)
J. Mol. Graph. Model.
, vol.22
, pp. 425-439
-
-
Okamoto, Y.1
-
25
-
-
40549088876
-
Prediction of protein loop conformations using multiscale modeling methods with physical energy scoring functions
-
Olson M.A., Feig M., and Brooks III C.L. Prediction of protein loop conformations using multiscale modeling methods with physical energy scoring functions. J. Comput. Chem. 29 (2008) 820-831
-
(2008)
J. Comput. Chem.
, vol.29
, pp. 820-831
-
-
Olson, M.A.1
Feig, M.2
Brooks III, C.L.3
-
26
-
-
1842479952
-
Exploring protein native states and large-scale conformational changes with a modified generalized Born model
-
Onufriev A., Bashford D., and Case D.A. Exploring protein native states and large-scale conformational changes with a modified generalized Born model. Proteins 55 (2004) 383-394
-
(2004)
Proteins
, vol.55
, pp. 383-394
-
-
Onufriev, A.1
Bashford, D.2
Case, D.A.3
-
27
-
-
33847254549
-
Replica exchange simulation of reversible folding/unfolding of the Trp-cage miniprotein in explicit solvent: on the structure and possible role of internal water
-
Paschek D., Nymeyer H., and Garcia A.E. Replica exchange simulation of reversible folding/unfolding of the Trp-cage miniprotein in explicit solvent: on the structure and possible role of internal water. J. Struct. Biol. 157 (2007) 524-533
-
(2007)
J. Struct. Biol.
, vol.157
, pp. 524-533
-
-
Paschek, D.1
Nymeyer, H.2
Garcia, A.E.3
-
28
-
-
15544384111
-
On the efficiency of exchange in parallel tempering Monte Carlo simulations
-
Predescu C., Predescu M., and Ciobanu C.V.J. On the efficiency of exchange in parallel tempering Monte Carlo simulations. J. Phys. Chem. B 109 (2005) 4189-4196
-
(2005)
J. Phys. Chem. B
, vol.109
, pp. 4189-4196
-
-
Predescu, C.1
Predescu, M.2
Ciobanu, C.V.J.3
-
29
-
-
22944453404
-
Optimal allocation of replicas in parallel tempering simulations
-
Rathore N., Chopra M., and de Pablo J.J. Optimal allocation of replicas in parallel tempering simulations. J. Chem. Phys. 122 (2005) 24111-24118
-
(2005)
J. Chem. Phys.
, vol.122
, pp. 24111-24118
-
-
Rathore, N.1
Chopra, M.2
de Pablo, J.J.3
-
30
-
-
0036467163
-
Structure of Met-enkephalin in explicit aqueous solution using replica exchange molecular dynamics
-
Sanbonmatsu K.Y., and Garcia A.E. Structure of Met-enkephalin in explicit aqueous solution using replica exchange molecular dynamics. Proteins Struct. Funct. Bioinform. 46 (2002) 225
-
(2002)
Proteins Struct. Funct. Bioinform.
, vol.46
, pp. 225
-
-
Sanbonmatsu, K.Y.1
Garcia, A.E.2
-
31
-
-
0001616080
-
Replica-exchange molecular dynamics method for protein folding
-
Sugita Y., and Okamoto Y. Replica-exchange molecular dynamics method for protein folding. Chem. Phys. Lett. 314 (1999) 141-151
-
(1999)
Chem. Phys. Lett.
, vol.314
, pp. 141-151
-
-
Sugita, Y.1
Okamoto, Y.2
-
32
-
-
35949020425
-
Replica Monte Carlo simulations of spin glasses
-
Swendsen R.H., and Wang J.S. Replica Monte Carlo simulations of spin glasses. Phys. Rev. Lett. 57 (1986) 2607-2609
-
(1986)
Phys. Rev. Lett.
, vol.57
, pp. 2607-2609
-
-
Swendsen, R.H.1
Wang, J.S.2
-
33
-
-
0038008976
-
An improved protein decoy set for testing energy functions for protein structure prediction
-
Tsai J., Bonneau R., Morozov AV., Kuhlman B., Rohl CA., and Baker D. An improved protein decoy set for testing energy functions for protein structure prediction. Proteins 53 (2003) 76-87
-
(2003)
Proteins
, vol.53
, pp. 76-87
-
-
Tsai, J.1
Bonneau, R.2
Morozov, AV.3
Kuhlman, B.4
Rohl, CA.5
Baker, D.6
-
34
-
-
33846207136
-
Replica-exchange molecular dynamics simulation of small peptide in water and in ethanol
-
Yoshida K., Yamaguchi T., and Okamoto Y. Replica-exchange molecular dynamics simulation of small peptide in water and in ethanol. Chem. Phys. Lett. 41 (2005) 2280-2284
-
(2005)
Chem. Phys. Lett.
, vol.41
, pp. 2280-2284
-
-
Yoshida, K.1
Yamaguchi, T.2
Okamoto, Y.3
-
35
-
-
0141704162
-
Free energy landscape of protein folding in water: explicit vs. implicit solvent
-
Zhou R. Free energy landscape of protein folding in water: explicit vs. implicit solvent. Proteins Struct. Funct. Bioinform. 53 (2003) 148-161
-
(2003)
Proteins Struct. Funct. Bioinform.
, vol.53
, pp. 148-161
-
-
Zhou, R.1
-
36
-
-
0036789950
-
Can a continuum solvent model reproduce the free energy landscape of a β-hairpin folding in water?
-
Zhou R., and Berne B.J. Can a continuum solvent model reproduce the free energy landscape of a β-hairpin folding in water?. Proc. Natl. Acad. Sci. USA 99 (2002) 12777-12782
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 12777-12782
-
-
Zhou, R.1
Berne, B.J.2
|