-
3
-
-
79956058665
-
Biomolecular modeling and simulation: A field coming of age
-
Schlick, T.; Collepardo-Guevara, R.; Halvorsen, L. A.; Jung, S.; Xiao, X. Biomolecular modeling and simulation: A field coming of age Q. Rev. Biophys. 2011, 44, 191-228
-
(2011)
Q. Rev. Biophys.
, vol.44
, pp. 191-228
-
-
Schlick, T.1
Collepardo-Guevara, R.2
Halvorsen, L.A.3
Jung, S.4
Xiao, X.5
-
4
-
-
64649101249
-
Long-timescale molecular dynamics simulations of protein structure and function
-
Klepeis, J. L.; Lindorff-Larsen, K.; Dror, R. O.; Shaw, D. E. Long-timescale molecular dynamics simulations of protein structure and function Curr. Opin. Struct. Biol. 2009, 19, 120-127
-
(2009)
Curr. Opin. Struct. Biol.
, vol.19
, pp. 120-127
-
-
Klepeis, J.L.1
Lindorff-Larsen, K.2
Dror, R.O.3
Shaw, D.E.4
-
5
-
-
0036280693
-
Protein and peptide folding explored with molecular simulations
-
Brooks, C. L. Protein and peptide folding explored with molecular simulations Acc. Chem. Res. 2002, 35, 447-454
-
(2002)
Acc. Chem. Res.
, vol.35
, pp. 447-454
-
-
Brooks, C.L.1
-
7
-
-
0034743155
-
From folding theories to folding proteins: A review and assessment of simulation studies of protein folding and unfolding
-
Shea, J. E.; Brooks, C. L. From folding theories to folding proteins: A review and assessment of simulation studies of protein folding and unfolding Annu. Rev. Phys. Chem. 2001, 52, 499-535
-
(2001)
Annu. Rev. Phys. Chem.
, vol.52
, pp. 499-535
-
-
Shea, J.E.1
Brooks, C.L.2
-
8
-
-
2142813682
-
Computer simulation of molecular dynamics: Methodology, applications and perspectives in chemistry
-
van Gunsteren, W. F.; Berendsen, H. J. C. Computer simulation of molecular dynamics: Methodology, applications and perspectives in chemistry Angew. Chem., Int. Ed. 1990, 29, 992-1023
-
(1990)
Angew. Chem., Int. Ed.
, vol.29
, pp. 992-1023
-
-
Van Gunsteren, W.F.1
Berendsen, H.J.C.2
-
9
-
-
0036725277
-
Molecular dynamics simulations of biomolecules
-
Karplus, M.; McCammon, J. A. Molecular dynamics simulations of biomolecules Nat. Struct. Biol. 2002, 9, 646-652
-
(2002)
Nat. Struct. Biol.
, vol.9
, pp. 646-652
-
-
Karplus, M.1
McCammon, J.A.2
-
10
-
-
77957572546
-
Challenges in protein-folding simulations
-
Freddolino, P. L.; Harrison, C. B.; Liu, Y.; Schulten, K. Challenges in protein-folding simulations Nat. Phys. 2010, 6, 751-758
-
(2010)
Nat. Phys.
, vol.6
, pp. 751-758
-
-
Freddolino, P.L.1
Harrison, C.B.2
Liu, Y.3
Schulten, K.4
-
11
-
-
84857033265
-
Atomistic molecular simulations of protein folding
-
Best, R. B. Atomistic molecular simulations of protein folding Curr. Opin. Struct. Biol. 2012, 22, 52-61
-
(2012)
Curr. Opin. Struct. Biol.
, vol.22
, pp. 52-61
-
-
Best, R.B.1
-
12
-
-
79955874370
-
Equilibrium sampling in biomolecular simulations
-
In; Rees, D. C. Dill, K. A. Williamson, J. R. Eds; Vol.
-
Zuckerman, D. M. Equilibrium sampling in biomolecular simulations. In Annu. Rev. Biophys.; Rees, D. C.; Dill, K. A.; Williamson, J. R., Eds; 2011; Vol. 40, pp 41-62.
-
(2011)
Annu. Rev. Biophys.
, vol.40
, pp. 41-62
-
-
Zuckerman, D.M.1
-
13
-
-
4444351490
-
Empirical force fields for biological macromolecules: Overview and issues
-
MacKerell, A. D. Empirical force fields for biological macromolecules: Overview and issues J. Comput. Chem. 2004, 25, 1584-1604
-
(2004)
J. Comput. Chem.
, vol.25
, pp. 1584-1604
-
-
Mackerell, A.D.1
-
14
-
-
34250312085
-
How sensitive are nanosecond molecular dynamics simulations of proteins to changes in the force field?
-
Villa, A.; Fan, H.; Wassenaar, T.; Mark, A. E. How sensitive are nanosecond molecular dynamics simulations of proteins to changes in the force field? J. Phys. Chem. B 2007, 111, 6015-6025
-
(2007)
J. Phys. Chem. B
, vol.111
, pp. 6015-6025
-
-
Villa, A.1
Fan, H.2
Wassenaar, T.3
Mark, A.E.4
-
15
-
-
84873719639
-
An overview of the Amber biomolecular simulation package
-
Salomon-Ferrer, R.; Case, D. A.; Walker, R. C. An overview of the Amber biomolecular simulation package Wiley Interdiscip. Rev.: Comput. Mol. Sci. 2013, 3, 198-210
-
(2013)
Wiley Interdiscip. Rev.: Comput. Mol. Sci.
, vol.3
, pp. 198-210
-
-
Salomon-Ferrer, R.1
Case, D.A.2
Walker, R.C.3
-
16
-
-
27344436659
-
Scalable molecular dynamics with NAMD
-
Phillips, J. C.; Braun, R.; Wang, W.; Gumbart, J.; Tajkhorshid, E.; Villa, E.; Chipot, C.; Skeel, R. D.; Kale, L.; Schulten, K. Scalable molecular dynamics with NAMD J. Comput. Chem. 2005, 26, 1781-1802
-
(2005)
J. Comput. Chem.
, vol.26
, pp. 1781-1802
-
-
Phillips, J.C.1
Braun, R.2
Wang, W.3
Gumbart, J.4
Tajkhorshid, E.5
Villa, E.6
Chipot, C.7
Skeel, R.D.8
Kale, L.9
Schulten, K.10
-
17
-
-
84875592758
-
GROMACS 4.5: A high-throughput and highly parallel open source molecular simulation toolkit
-
Pronk, S.; Pall, S.; Schulz, R.; Larsson, P.; Bjelkmar, P.; Apostolov, R.; Shirts, M. R.; Smith, J. C.; Kasson, P. M.; van der Spoel, D.; Hess, B.; Lindahl, E. GROMACS 4.5: A high-throughput and highly parallel open source molecular simulation toolkit Bioinformatics 2013, 29, 845-854
-
(2013)
Bioinformatics
, vol.29
, pp. 845-854
-
-
Pronk, S.1
Pall, S.2
Schulz, R.3
Larsson, P.4
Bjelkmar, P.5
Apostolov, R.6
Shirts, M.R.7
Smith, J.C.8
Kasson, P.M.9
Van Der Spoel, D.10
Hess, B.11
Lindahl, E.12
-
18
-
-
69349101503
-
Quantifying uncertainty and sampling quality in biomolecular simulations
-
Grossfield, A.; Zuckerman, D. M. Quantifying uncertainty and sampling quality in biomolecular simulations Annu. Rep. Comput. Chem. 2009, 5, 23-48
-
(2009)
Annu. Rep. Comput. Chem.
, vol.5
, pp. 23-48
-
-
Grossfield, A.1
Zuckerman, D.M.2
-
19
-
-
84873526912
-
To milliseconds and beyond: Challenges in the simulation of protein folding
-
Lane, T. J.; Shukla, D.; Beauchamp, K. A.; Pande, V. S. To milliseconds and beyond: Challenges in the simulation of protein folding Curr. Opin. Struct. Biol. 2013, 23, 58-65
-
(2013)
Curr. Opin. Struct. Biol.
, vol.23
, pp. 58-65
-
-
Lane, T.J.1
Shukla, D.2
Beauchamp, K.A.3
Pande, V.S.4
-
20
-
-
80055081145
-
How fast-folding proteins fold
-
Lindorff-Larsen, K.; Piana, S.; Dror, R. O.; Shaw, D. E. How fast-folding proteins fold Science 2011, 334, 517-520
-
(2011)
Science
, vol.334
, pp. 517-520
-
-
Lindorff-Larsen, K.1
Piana, S.2
Dror, R.O.3
Shaw, D.E.4
-
21
-
-
77953508894
-
Microsecond simulations of the folding/unfolding thermodynamics of the trp-cage miniprotein
-
Day, R.; Paschek, D.; Garcia, A. E. Microsecond simulations of the folding/unfolding thermodynamics of the trp-cage miniprotein Proteins: Struct., Funct., Bioinf. 2010, 78, 1889-1899
-
(2010)
Proteins: Struct., Funct., Bioinf.
, vol.78
, pp. 1889-1899
-
-
Day, R.1
Paschek, D.2
Garcia, A.E.3
-
22
-
-
0001616080
-
Replica-exchange molecular dynamics method for protein folding
-
Sugita, Y.; Okamoto, Y. Replica-exchange molecular dynamics method for protein folding Chem. Phys. Lett. 1999, 314, 141-151
-
(1999)
Chem. Phys. Lett.
, vol.314
, pp. 141-151
-
-
Sugita, Y.1
Okamoto, Y.2
-
24
-
-
79959713919
-
Definition and testing of the GROMOS force-field versions 54A7 and 54B7
-
Schmid, N.; Eichenberger, A. P.; Choutko, A.; Riniker, S.; Winger, M.; Mark, A. E.; van Gunsteren, W. F. Definition and testing of the GROMOS force-field versions 54A7 and 54B7 Eur. Biophys. J. Biophys. Lett. 2011, 40, 843-856
-
(2011)
Eur. Biophys. J. Biophys. Lett.
, vol.40
, pp. 843-856
-
-
Schmid, N.1
Eichenberger, A.P.2
Choutko, A.3
Riniker, S.4
Winger, M.5
Mark, A.E.6
Van Gunsteren, W.F.7
-
25
-
-
84867344848
-
New interaction parameters for charged amino acid side chains in the GROMOS force field
-
Reif, M. M.; Huenenberger, P. H.; Oostenbrink, C. New interaction parameters for charged amino acid side chains in the GROMOS force field J. Chem. Theory Comput. 2012, 8, 3705-3723
-
(2012)
J. Chem. Theory Comput.
, vol.8
, pp. 3705-3723
-
-
Reif, M.M.1
Huenenberger, P.H.2
Oostenbrink, C.3
-
26
-
-
1642576012
-
Improved treatment of the protein backbone in empirical force fields
-
MacKerell, A. D.; Feig, M.; Brooks, C. L. Improved treatment of the protein backbone in empirical force fields J. Am. Chem. Soc. 2004, 126, 698-699
-
(2004)
J. Am. Chem. Soc.
, vol.126
, pp. 698-699
-
-
Mackerell, A.D.1
Feig, M.2
Brooks, C.L.3
-
27
-
-
84865723813
-
Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone phi, psi and side-chain chi(1) and chi(2) dihedral angles
-
Best, R. B.; Zhu, X.; Shim, J.; Lopes, P. E. M.; Mittal, J.; Feig, M.; MacKerell, A. D., Jr. Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone phi, psi and side-chain chi(1) and chi(2) dihedral angles J. Chem. Theory Comput. 2012, 8, 3257-3273
-
(2012)
J. Chem. Theory Comput.
, vol.8
, pp. 3257-3273
-
-
Best, R.B.1
Zhu, X.2
Shim, J.3
Lopes, P.E.M.4
Mittal, J.5
Feig, M.6
Mackerell Jr., A.D.7
-
28
-
-
77953513118
-
Improved side-chain torsion potentials for the Amber ff99SB protein force field
-
Lindorff-Larsen, K.; Piana, S.; Palmo, K.; Maragakis, P.; Klepeis, J. L.; Dror, R. O.; Shaw, D. E. Improved side-chain torsion potentials for the Amber ff99SB protein force field Proteins: Struct., Funct., Bioinf. 2010, 78, 1950-1958
-
(2010)
Proteins: Struct., Funct., Bioinf.
, vol.78
, pp. 1950-1958
-
-
Lindorff-Larsen, K.1
Piana, S.2
Palmo, K.3
Maragakis, P.4
Klepeis, J.L.5
Dror, R.O.6
Shaw, D.E.7
-
29
-
-
77956606590
-
NMR-based protein potentials
-
Li, D.-W.; Brueschweiler, R. NMR-based protein potentials Angew. Chem., Int. Ed. 2010, 49, 6778-6780
-
(2010)
Angew. Chem., Int. Ed.
, vol.49
, pp. 6778-6780
-
-
Li, D.-W.1
Brueschweiler, R.2
-
30
-
-
33748518255
-
Comparison of multiple Amber force fields and development of improved protein backbone parameters
-
Hornak, V.; Abel, R.; Okur, A.; Strockbine, B.; Roitberg, A.; Simmerling, C. Comparison of multiple Amber force fields and development of improved protein backbone parameters Proteins: Struct., Funct., Bioinf. 2006, 65, 712-725
-
(2006)
Proteins: Struct., Funct., Bioinf.
, vol.65
, pp. 712-725
-
-
Hornak, V.1
Abel, R.2
Okur, A.3
Strockbine, B.4
Roitberg, A.5
Simmerling, C.6
-
31
-
-
67649494492
-
Optimized molecular dynamics force fields applied to the helix-coil transition of polypeptides
-
Best, R. B.; Hummer, G. Optimized molecular dynamics force fields applied to the helix-coil transition of polypeptides J. Phys. Chem. B 2009, 113, 9004-9015
-
(2009)
J. Phys. Chem. B
, vol.113
, pp. 9004-9015
-
-
Best, R.B.1
Hummer, G.2
-
32
-
-
20544435097
-
Exploring the helix-coil transition via all-atom equilibrium ensemble simulations
-
Sorin, E. J.; Pande, V. S. Exploring the helix-coil transition via all-atom equilibrium ensemble simulations Biophys. J. 2005, 88, 2472-2493
-
(2005)
Biophys. J.
, vol.88
, pp. 2472-2493
-
-
Sorin, E.J.1
Pande, V.S.2
-
33
-
-
67650359927
-
Force field bias in protein folding simulations
-
Freddolino, P. L.; Park, S.; Roux, B.; Schulten, K. Force field bias in protein folding simulations Biophys. J. 2009, 96, 3772-3780
-
(2009)
Biophys. J.
, vol.96
, pp. 3772-3780
-
-
Freddolino, P.L.1
Park, S.2
Roux, B.3
Schulten, K.4
-
34
-
-
46749127364
-
Are current molecular dynamics force fields too helical?
-
Best, R. B.; Buchete, N.-V.; Hummer, G. Are current molecular dynamics force fields too helical? Biophys. J. 2008, 95, L7-L9
-
(2008)
Biophys. J.
, vol.95
-
-
Best, R.B.1
Buchete, N.-V.2
Hummer, G.3
-
35
-
-
68949107624
-
Secondary structure propensities in peptide folding simulations: A systematic comparison of molecular mechanics interaction schemes
-
Matthes, D.; de Groot, B. L. Secondary structure propensities in peptide folding simulations: A systematic comparison of molecular mechanics interaction schemes Biophys. J. 2009, 97, 599-608
-
(2009)
Biophys. J.
, vol.97
, pp. 599-608
-
-
Matthes, D.1
De Groot, B.L.2
-
36
-
-
77956302920
-
Evaluating molecular mechanical potentials for helical peptides and proteins
-
Thompson, E. J.; DePaul, A. J.; Patel, S. S.; Sorin, E. J. Evaluating molecular mechanical potentials for helical peptides and proteins PLoS One 2010, 5, e10056
-
(2010)
PLoS One
, vol.5
, pp. 10056
-
-
Thompson, E.J.1
Depaul, A.J.2
Patel, S.S.3
Sorin, E.J.4
-
37
-
-
79959720287
-
How robust are protein folding simulations with respect to force field parameterization?
-
Piana, S.; Lindorff-Larsen, K.; Shaw, D. E. How robust are protein folding simulations with respect to force field parameterization? Biophys. J. 2011, 100, L47-L49
-
(2011)
Biophys. J.
, vol.100
-
-
Piana, S.1
Lindorff-Larsen, K.2
Shaw, D.E.3
-
38
-
-
79954518426
-
Optimizing protein-solvent force fields to reproduce intrinsic conformational preferences of model peptides
-
Nerenberg, P. S.; Head-Gordon, T. Optimizing protein-solvent force fields to reproduce intrinsic conformational preferences of model peptides J. Chem. Theory Comput. 2011, 7, 1220-1230
-
(2011)
J. Chem. Theory Comput.
, vol.7
, pp. 1220-1230
-
-
Nerenberg, P.S.1
Head-Gordon, T.2
-
39
-
-
84868122477
-
Simple few-state models reveal hidden complexity in protein folding
-
Beauchamp, K. A.; McGibbon, R.; Lin, Y.-S.; Pande, V. S. Simple few-state models reveal hidden complexity in protein folding Proc. Natl. Acad. Sci. U.S.A. 2012, 109, 17807-17813
-
(2012)
Proc. Natl. Acad. Sci. U.S.A.
, vol.109
, pp. 17807-17813
-
-
Beauchamp, K.A.1
McGibbon, R.2
Lin, Y.-S.3
Pande, V.S.4
-
40
-
-
84859910432
-
Force-field dependence of chignolin folding and misfolding: Comparison with experiment and redesign
-
Kuhrova, P.; De Simone, A.; Otyepka, M.; Best, R. B. Force-field dependence of chignolin folding and misfolding: comparison with experiment and redesign Biophys. J. 2012, 102, 1897-1906
-
(2012)
Biophys. J.
, vol.102
, pp. 1897-1906
-
-
Kuhrova, P.1
De Simone, A.2
Otyepka, M.3
Best, R.B.4
-
41
-
-
84856728860
-
Microsecond time-scale conformational exchange in proteins: Using long molecular dynamics trajectory to simulate nmr relaxation dispersion data
-
Xue, Y.; Ward, J. M.; Yuwen, T.; Podkorytov, I. S.; Skrynnikov, N. R. Microsecond time-scale conformational exchange in proteins: Using long molecular dynamics trajectory to simulate nmr relaxation dispersion data J. Am. Chem. Soc. 2012, 134, 2555-2562
-
(2012)
J. Am. Chem. Soc.
, vol.134
, pp. 2555-2562
-
-
Xue, Y.1
Ward, J.M.2
Yuwen, T.3
Podkorytov, I.S.4
Skrynnikov, N.R.5
-
42
-
-
79955395931
-
What is the time scale for alpha-helix nucleation?
-
De Sancho, D.; Best, R. B. What is the time scale for alpha-helix nucleation? J. Am. Chem. Soc. 2011, 133, 6809-6816
-
(2011)
J. Am. Chem. Soc.
, vol.133
, pp. 6809-6816
-
-
De Sancho, D.1
Best, R.B.2
-
43
-
-
80053632403
-
Speed limit of protein folding evidenced in secondary structure dynamics
-
Lin, M. M.; Mohammed, O. F.; Jas, G. S.; Zewail, A. H. Speed limit of protein folding evidenced in secondary structure dynamics Proc. Natl. Acad. Sci. U.S.A. 2011, 108, 16622-16627
-
(2011)
Proc. Natl. Acad. Sci. U.S.A.
, vol.108
, pp. 16622-16627
-
-
Lin, M.M.1
Mohammed, O.F.2
Jas, G.S.3
Zewail, A.H.4
-
44
-
-
80052801453
-
Bridging the gap between folding simulations and experiments: The case of the villin headpiece
-
Saladino, G.; Marenchino, M.; Gervasio, F. L. Bridging the gap between folding simulations and experiments: The case of the villin headpiece J. Chem. Theory Comput. 2011, 7, 2675-2680
-
(2011)
J. Chem. Theory Comput.
, vol.7
, pp. 2675-2680
-
-
Saladino, G.1
Marenchino, M.2
Gervasio, F.L.3
-
45
-
-
78649551877
-
Protein simulations with an optimized water model: Cooperative helix formation and temperature-induced unfolded state collapse
-
Best, R. B.; Mittal, J. Protein simulations with an optimized water model: Cooperative helix formation and temperature-induced unfolded state collapse J. Phys. Chem. B 2010, 114, 14916-14923
-
(2010)
J. Phys. Chem. B
, vol.114
, pp. 14916-14923
-
-
Best, R.B.1
Mittal, J.2
-
46
-
-
77954320896
-
Balance between alpha and beta structures in ab initio protein folding
-
Best, R. B.; Mittal, J. Balance between alpha and beta structures in ab initio protein folding J. Phys. Chem. B 2010, 114, 8790-8798
-
(2010)
J. Phys. Chem. B
, vol.114
, pp. 8790-8798
-
-
Best, R.B.1
Mittal, J.2
-
47
-
-
84872838664
-
Validation of the GROMOS 54A7 force field regarding mixed alpha/beta-peptide molecules
-
Wang, D.; Freitag, F.; Gattin, Z.; Haberkern, H.; Jaun, B.; Siwko, M.; Vyas, R.; van Gunsteren, W. F.; Dolenc, J. Validation of the GROMOS 54A7 force field regarding mixed alpha/beta-peptide molecules Helv. Chim. Acta 2012, 95, 2562-2577
-
(2012)
Helv. Chim. Acta
, vol.95
, pp. 2562-2577
-
-
Wang, D.1
Freitag, F.2
Gattin, Z.3
Haberkern, H.4
Jaun, B.5
Siwko, M.6
Vyas, R.7
Van Gunsteren, W.F.8
Dolenc, J.9
-
48
-
-
14844303886
-
Single turn peptide alpha helices with exceptional stability in water
-
Shepherd, N. E.; Hoang, H. N.; Abbenante, G.; Fairlie, D. P. Single turn peptide alpha helices with exceptional stability in water J. Am. Chem. Soc. 2005, 127, 2974-2983
-
(2005)
J. Am. Chem. Soc.
, vol.127
, pp. 2974-2983
-
-
Shepherd, N.E.1
Hoang, H.N.2
Abbenante, G.3
Fairlie, D.P.4
-
49
-
-
79958220797
-
Direct assessment of the alpha-helix nucleation time
-
Serrano, A. L.; Tucker, M. J.; Gai, F. Direct assessment of the alpha-helix nucleation time J. Phys. Chem. B 2011, 115, 7472-7478
-
(2011)
J. Phys. Chem. B
, vol.115
, pp. 7472-7478
-
-
Serrano, A.L.1
Tucker, M.J.2
Gai, F.3
-
50
-
-
0002775934
-
Interaction models for water in relation to protein hydration
-
In; Pullman, B. D. Reidel Publishing: Dordrecht, Holland
-
Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; Hermans, J. Interaction models for water in relation to protein hydration. In Intermolecular Forces; Pullman, B., Ed.; D. Reidel Publishing: Dordrecht, Holland, 1981; pp 331-342.
-
(1981)
Intermolecular Forces
, pp. 331-342
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
Van Gunsteren, W.F.3
Hermans, J.4
-
51
-
-
33750587438
-
Molecular dynamics with coupling to an external bath
-
Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; Dinola, A.; Haak, J. R. Molecular dynamics with coupling to an external bath J. Chem. Phys. 1984, 81, 3684-3690
-
(1984)
J. Chem. Phys.
, vol.81
, pp. 3684-3690
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
Van Gunsteren, W.F.3
Dinola, A.4
Haak, J.R.5
-
52
-
-
0001158363
-
Monte Carlo studies of dielectric properties of water-like models
-
Barker, J. A.; Watts, R. O. Monte Carlo studies of dielectric properties of water-like models Mol. Phys. 1973, 26, 789-792
-
(1973)
Mol. Phys.
, vol.26
, pp. 789-792
-
-
Barker, J.A.1
Watts, R.O.2
-
53
-
-
2242491482
-
Consistent dielectric properties of the simple point-charge and extended simple point-charge water models at 277 and 300 K
-
Smith, P. E.; van Gunsteren, W. F. Consistent dielectric properties of the simple point-charge and extended simple point-charge water models at 277 and 300 K J. Chem. Phys. 1994, 100, 3169-3174
-
(1994)
J. Chem. Phys.
, vol.100
, pp. 3169-3174
-
-
Smith, P.E.1
Van Gunsteren, W.F.2
-
54
-
-
38749123962
-
P-LINCS: A parallel linear constraint solver for molecular simulation
-
Hess, B. P-LINCS: A parallel linear constraint solver for molecular simulation J. Chem. Theory Comput. 2008, 4, 116-122
-
(2008)
J. Chem. Theory Comput.
, vol.4
, pp. 116-122
-
-
Hess, B.1
-
55
-
-
84986440341
-
SETTLE: An analytical version of the SHAKE and RATTLE algorithm for rigid water models
-
Miyamoto, S.; Kollman, P. A. SETTLE: An analytical version of the SHAKE and RATTLE algorithm for rigid water models J. Comput. Chem. 1992, 13, 952-962
-
(1992)
J. Comput. Chem.
, vol.13
, pp. 952-962
-
-
Miyamoto, S.1
Kollman, P.A.2
-
56
-
-
79953908369
-
Unfolding the conformational behavior of peptide dendrimers: Insights from molecular dynamics simulations
-
Filipe, L. C. S.; Machuqueiro, M.; Baptista, A. M. Unfolding the conformational behavior of peptide dendrimers: Insights from molecular dynamics simulations J. Am. Chem. Soc. 2011, 133, 5042-5052
-
(2011)
J. Am. Chem. Soc.
, vol.133
, pp. 5042-5052
-
-
Filipe, L.C.S.1
Machuqueiro, M.2
Baptista, A.M.3
-
57
-
-
33846086933
-
Canonical sampling through velocity rescaling
-
Bussi, G.; Donadio, D.; Parrinello, M. Canonical sampling through velocity rescaling J. Chem. Phys. 2007, 126, 014101
-
(2007)
J. Chem. Phys.
, vol.126
, pp. 014101
-
-
Bussi, G.1
Donadio, D.2
Parrinello, M.3
-
58
-
-
41549127613
-
A temperature predictor for parallel tempering simulations
-
Patriksson, A.; van der Spoel, D. A temperature predictor for parallel tempering simulations Phys. Chem. Chem. Phys. 2008, 10, 2073-2077
-
(2008)
Phys. Chem. Chem. Phys.
, vol.10
, pp. 2073-2077
-
-
Patriksson, A.1
Van Der Spoel, D.2
-
59
-
-
84875760613
-
Metadynamics
-
Barducci, A.; Bonomi, M.; Parrinello, M. Metadynamics Wiley Interdiscip. Rev.: Comput. Mol. Sci. 2011, 1, 826-843
-
(2011)
Wiley Interdiscip. Rev.: Comput. Mol. Sci.
, vol.1
, pp. 826-843
-
-
Barducci, A.1
Bonomi, M.2
Parrinello, M.3
-
60
-
-
34249071886
-
A bias-exchange approach to protein folding
-
Piana, S.; Laio, A. A bias-exchange approach to protein folding J. Phys. Chem. B 2007, 111, 4553-4559
-
(2007)
J. Phys. Chem. B
, vol.111
, pp. 4553-4559
-
-
Piana, S.1
Laio, A.2
-
61
-
-
69349100797
-
PLUMED: A portable plugin for free-energy calculations with molecular dynamics
-
Bonomi, M.; Branduardi, D.; Bussi, G.; Camilloni, C.; Provasi, D.; Raiteri, P.; Donadio, D.; Marinelli, F.; Pietrucci, F.; Broglia, R. A.; Parrinello, M. PLUMED: A portable plugin for free-energy calculations with molecular dynamics Comput. Phys. Commun. 2009, 180, 1961-1972
-
(2009)
Comput. Phys. Commun.
, vol.180
, pp. 1961-1972
-
-
Bonomi, M.1
Branduardi, D.2
Bussi, G.3
Camilloni, C.4
Provasi, D.5
Raiteri, P.6
Donadio, D.7
Marinelli, F.8
Pietrucci, F.9
Broglia, R.A.10
Parrinello, M.11
-
62
-
-
0003946510
-
-
2 nd ed. Springer: New York, pp and 111-133
-
Jolliffe, I. T. Principal Component Analysis, 2 nd ed.; Springer: New York, 2002; pp 1-9 and 111-133.
-
(2002)
Principal Component Analysis
, pp. 1-9
-
-
Jolliffe, I.T.1
-
63
-
-
71549167017
-
Conformational analysis in a multidimensional energy landscape: Study of an arginylglutamate repeat
-
Campos, S. R. R.; Baptista, A. M. Conformational analysis in a multidimensional energy landscape: Study of an arginylglutamate repeat J. Phys. Chem. B 2009, 113, 15989-16001
-
(2009)
J. Phys. Chem. B
, vol.113
, pp. 15989-16001
-
-
Campos, S.R.R.1
Baptista, A.M.2
-
65
-
-
79957488000
-
Markov models of molecular kinetics: Generation and validation
-
Prinz, J.-H.; Wu, H.; Sarich, M.; Keller, B.; Senne, M.; Held, M.; Chodera, J. D.; Schuette, C.; Noe, F. Markov models of molecular kinetics: Generation and validation J. Chem. Phys. 2011, 134, 174105
-
(2011)
J. Chem. Phys.
, vol.134
, pp. 174105
-
-
Prinz, J.-H.1
Wu, H.2
Sarich, M.3
Keller, B.4
Senne, M.5
Held, M.6
Chodera, J.D.7
Schuette, C.8
Noe, F.9
-
66
-
-
0020997912
-
Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
-
Kabsch, W.; Sander, C. Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features Biopolymers 1983, 22, 2577-2637
-
(1983)
Biopolymers
, vol.22
, pp. 2577-2637
-
-
Kabsch, W.1
Sander, C.2
-
67
-
-
10844292652
-
Energy landscape of a small peptide revealed by dihedral angle principal component analysis
-
Mu, Y. G.; Nguyen, P. H.; Stock, G. Energy landscape of a small peptide revealed by dihedral angle principal component analysis Proteins: Struct., Funct., Bioinf. 2005, 58, 45-52
-
(2005)
Proteins: Struct., Funct., Bioinf.
, vol.58
, pp. 45-52
-
-
Mu, Y.G.1
Nguyen, P.H.2
Stock, G.3
-
68
-
-
44949178407
-
Coarse master equations for peptide folding dynamics
-
Buchete, N.-V.; Hummer, G. Coarse master equations for peptide folding dynamics J. Phys. Chem. B 2008, 112, 6057-6069
-
(2008)
J. Phys. Chem. B
, vol.112
, pp. 6057-6069
-
-
Buchete, N.-V.1
Hummer, G.2
-
69
-
-
70450255797
-
Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations
-
Noe, F.; Schuette, C.; Vanden-Eijnden, E.; Reich, L.; Weikl, T. R. Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 19011-19016
-
(2009)
Proc. Natl. Acad. Sci. U.S.A.
, vol.106
, pp. 19011-19016
-
-
Noe, F.1
Schuette, C.2
Vanden-Eijnden, E.3
Reich, L.4
Weikl, T.R.5
-
70
-
-
77954635393
-
Protein folded states are kinetic hubs
-
Bowman, G.; Pande, V. Protein folded states are kinetic hubs Proc. Natl. Acad. Sci. U.S.A. 2010, 107, 10890-10895
-
(2010)
Proc. Natl. Acad. Sci. U.S.A.
, vol.107
, pp. 10890-10895
-
-
Bowman, G.1
Pande, V.2
-
71
-
-
2942567954
-
Describing protein folding kinetics by molecular dynamics simulations. 1. Theory
-
Swope, W. C.; Pitera, J. W.; Suits, F. Describing protein folding kinetics by molecular dynamics simulations. 1. Theory J. Phys. Chem. B 2004, 108, 6571-6581
-
(2004)
J. Phys. Chem. B
, vol.108
, pp. 6571-6581
-
-
Swope, W.C.1
Pitera, J.W.2
Suits, F.3
-
72
-
-
69049099679
-
A kinetic model of trp-cage folding from multiple biased molecular dynamics simulations
-
Marinelli, F.; Pietrucci, F.; Laio, A.; Piana, S. A kinetic model of trp-cage folding from multiple biased molecular dynamics simulations PLoS Comput. Biol. 2009, 5, e1000452
-
(2009)
PLoS Comput. Biol.
, vol.5
, pp. 1000452
-
-
Marinelli, F.1
Pietrucci, F.2
Laio, A.3
Piana, S.4
|