Format
Sort by
Items per page

Send to

Choose Destination

Links from PubMed

Items: 1 to 20 of 99

1.

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
2.

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
3.

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
4.

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
5.

Essential slow degrees of freedom in protein-surface simulations: A metadynamics investigation.

Prakash A, Sprenger KG, Pfaendtner J.

Biochem Biophys Res Commun. 2018 Mar 29;498(2):274-281. doi: 10.1016/j.bbrc.2017.07.066. Epub 2017 Jul 15.

PMID:
28720500
6.

From metadynamics to dynamics.

Tiwary P, Parrinello M.

Phys Rev Lett. 2013 Dec 6;111(23):230602. Epub 2013 Dec 3.

PMID:
24476246
7.

Metadynamics Enhanced Markov Modeling of Protein Dynamics.

Biswas M, Lickert B, Stock G.

J Phys Chem B. 2018 May 31;122(21):5508-5514. doi: 10.1021/acs.jpcb.7b11800. Epub 2018 Jan 27.

PMID:
29338243
8.

Metadynamics convergence law in a multidimensional system.

Crespo Y, Marinelli F, Pietrucci F, Laio A.

Phys Rev E Stat Nonlin Soft Matter Phys. 2010 May;81(5 Pt 2):055701. Epub 2010 May 7.

PMID:
20866290
9.

Slow dynamics in protein fluctuations revealed by time-structure based independent component analysis: the case of domain motions.

Naritomi Y, Fuchigami S.

J Chem Phys. 2011 Feb 14;134(6):065101. doi: 10.1063/1.3554380.

PMID:
21322734
10.

Spectral gap optimization of order parameters for sampling complex molecular systems.

Tiwary P, Berne BJ.

Proc Natl Acad Sci U S A. 2016 Mar 15;113(11):2839-44. doi: 10.1073/pnas.1600917113. Epub 2016 Feb 29.

11.

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
12.

Molecular recognition of DNA by ligands: roughness and complexity of the free energy profile.

Zheng W, Vargiu AV, Rohrdanz MA, Carloni P, Clementi C.

J Chem Phys. 2013 Oct 14;139(14):145102. doi: 10.1063/1.4824106. Erratum in: J Chem Phys. 2013 Dec 14;139(22):229901. Vargiu, Attlio Vittorio [corrected to Vargiu, Attilio Vittorio].

13.

A variational conformational dynamics approach to the selection of collective variables in metadynamics.

McCarty J, Parrinello M.

J Chem Phys. 2017 Nov 28;147(20):204109. doi: 10.1063/1.4998598.

PMID:
29195289
14.

A time-independent free energy estimator for metadynamics.

Tiwary P, Parrinello M.

J Phys Chem B. 2015 Jan 22;119(3):736-42. doi: 10.1021/jp504920s. Epub 2014 Jul 21.

PMID:
25046020
15.

Modeling molecular kinetics with tICA and the kernel trick.

Schwantes CR, Pande VS.

J Chem Theory Comput. 2015 Feb 10;11(2):600-8. doi: 10.1021/ct5007357.

16.

Exploring free energy landscapes of large conformational changes: molecular dynamics with excited normal modes.

Costa MG, Batista PR, Bisch PM, Perahia D.

J Chem Theory Comput. 2015 Jun 9;11(6):2755-67. doi: 10.1021/acs.jctc.5b00003.

PMID:
26575568
17.

Insights into Stability and Folding of GNRA and UNCG Tetraloops Revealed by Microsecond Molecular Dynamics and Well-Tempered Metadynamics.

Haldar S, Kührová P, Banáš P, Spiwok V, Šponer J, Hobza P, Otyepka M.

J Chem Theory Comput. 2015 Aug 11;11(8):3866-77. doi: 10.1021/acs.jctc.5b00010.

PMID:
26574468
18.

Nonlinear vs. linear biasing in Trp-cage folding simulations.

Spiwok V, Oborský P, Pazúriková J, Křenek A, Králová B.

J Chem Phys. 2015 Mar 21;142(11):115101. doi: 10.1063/1.4914828.

PMID:
25796266
19.

Accelerating the Conformational Sampling of Intrinsically Disordered Proteins.

Do TN, Choy WY, Karttunen M.

J Chem Theory Comput. 2014 Nov 11;10(11):5081-94. doi: 10.1021/ct5004803.

PMID:
26584388
20.

Reducing the number of mean-square deviation calculations with floating close structure in metadynamics.

Pazúriková J, Křenek A, Spiwok V, Šimková M.

J Chem Phys. 2017 Mar 21;146(11):115101. doi: 10.1063/1.4978296.

PMID:
28330370

Supplemental Content

Support Center