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Items: 1 to 20 of 105

1.

Transfer Learning from Markov Models Leads to Efficient Sampling of Related Systems.

Sultan MM, Pande VS.

J Phys Chem B. 2018 May 31;122(21):5291-5299. doi: 10.1021/acs.jpcb.7b06896. Epub 2017 Oct 3.

PMID:
28938073
2.

tICA-Metadynamics: Accelerating Metadynamics by Using Kinetically Selected Collective Variables.

M Sultan M, Pande VS.

J Chem Theory Comput. 2017 Jun 13;13(6):2440-2447. doi: 10.1021/acs.jctc.7b00182. Epub 2017 May 9.

PMID:
28383914
3.

Transferable Neural Networks for Enhanced Sampling of Protein Dynamics.

Sultan MM, Wayment-Steele HK, Pande VS.

J Chem Theory Comput. 2018 Apr 10;14(4):1887-1894. doi: 10.1021/acs.jctc.8b00025. Epub 2018 Mar 19.

PMID:
29529369
4.

Variational Koopman models: Slow collective variables and molecular kinetics from short off-equilibrium simulations.

Wu H, Nüske F, Paul F, Klus S, Koltai P, Noé F.

J Chem Phys. 2017 Apr 21;146(15):154104. doi: 10.1063/1.4979344.

PMID:
28433026
5.

Comparison of Secondary Structure Formation Using 10 Different Force Fields in Microsecond Molecular Dynamics Simulations.

Cino EA, Choy WY, Karttunen M.

J Chem Theory Comput. 2012 Aug 14;8(8):2725-2740. Epub 2012 Jun 19.

6.

Refining Collective Coordinates and Improving Free Energy Representation in Variational Enhanced Sampling.

Yang YI, Parrinello M.

J Chem Theory Comput. 2018 Jun 12;14(6):2889-2894. doi: 10.1021/acs.jctc.8b00231. Epub 2018 May 11.

PMID:
29715017
7.

Free energy simulations with the AMOEBA polarizable force field and metadynamics on GPU platform.

Peng X, Zhang Y, Chu H, Li G.

J Comput Chem. 2016 Mar 5;37(6):614-22. doi: 10.1002/jcc.24227. Epub 2015 Oct 23.

PMID:
26493154
8.

Effects of force fields on the conformational and dynamic properties of amyloid β(1-40) dimer explored by replica exchange molecular dynamics simulations.

Watts CR, Gregory A, Frisbie C, Lovas S.

Proteins. 2018 Mar;86(3):279-300. doi: 10.1002/prot.25439. Epub 2017 Dec 25.

PMID:
29235155
9.

Macromolecular crowding: chemistry and physics meet biology (Ascona, Switzerland, 10-14 June 2012).

Foffi G, Pastore A, Piazza F, Temussi PA.

Phys Biol. 2013 Aug 2;10(4):040301. [Epub ahead of print]

PMID:
23912807
10.

Multiensemble Markov models of molecular thermodynamics and kinetics.

Wu H, Paul F, Wehmeyer C, Noé F.

Proc Natl Acad Sci U S A. 2016 Jun 7;113(23):E3221-30. doi: 10.1073/pnas.1525092113. Epub 2016 May 25. Erratum in: Proc Natl Acad Sci U S A. 2017 Jul 24;:.

11.

Are Protein Force Fields Getting Better? A Systematic Benchmark on 524 Diverse NMR Measurements.

Beauchamp KA, Lin YS, Das R, Pande VS.

J Chem Theory Comput. 2012 Apr 10;8(4):1409-1414. Epub 2012 Mar 12.

12.

Accelerated Molecular Dynamics Simulations with the AMOEBA Polarizable Force Field on Graphics Processing Units.

Lindert S, Bucher D, Eastman P, Pande V, McCammon JA.

J Chem Theory Comput. 2013 Nov 12;9(11):4684-4691. Epub 2013 Oct 15.

13.
14.

Toward a predictive understanding of slow methyl group dynamics in proteins.

Long D, Li DW, Walter KF, Griesinger C, Brüschweiler R.

Biophys J. 2011 Aug 17;101(4):910-5. doi: 10.1016/j.bpj.2011.06.053.

15.

Modeling and enhanced sampling of molecular systems with smooth and nonlinear data-driven collective variables.

Hashemian B, Millán D, Arroyo M.

J Chem Phys. 2013 Dec 7;139(21):214101. doi: 10.1063/1.4830403.

PMID:
24320358
16.

Metadynamics in essential coordinates: free energy simulation of conformational changes.

Spiwok V, Lipovová P, Králová B.

J Phys Chem B. 2007 Mar 29;111(12):3073-6. Epub 2007 Mar 6.

PMID:
17388445
17.

Structural Ensemble of CD4 Cytoplasmic Tail (402-419) Reveals a Nearly Flat Free-Energy Landscape with Local α-Helical Order in Aqueous Solution.

Ahalawat N, Arora S, Murarka RK.

J Phys Chem B. 2015 Aug 27;119(34):11229-42. doi: 10.1021/acs.jpcb.5b03092. Epub 2015 Jul 15.

PMID:
26132982
18.

Dynamic properties of force fields.

Vitalini F, Mey AS, Noé F, Keller BG.

J Chem Phys. 2015 Feb 28;142(8):084101. doi: 10.1063/1.4909549.

PMID:
25725706
19.

A Bayesian method for construction of Markov models to describe dynamics on various time-scales.

Rains EK, Andersen HC.

J Chem Phys. 2010 Oct 14;133(14):144113. doi: 10.1063/1.3496438.

PMID:
20949993
20.

Assessing the Current State of Amber Force Field Modifications for DNA.

Galindo-Murillo R, Robertson JC, Zgarbová M, Šponer J, Otyepka M, Jurečka P, Cheatham TE 3rd.

J Chem Theory Comput. 2016 Aug 9;12(8):4114-27. doi: 10.1021/acs.jctc.6b00186. Epub 2016 Jul 7.

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