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Items: 1 to 20 of 94

1.

Note: MSM lag time cannot be used for variational model selection.

Husic BE, Pande VS.

J Chem Phys. 2017 Nov 7;147(17):176101. doi: 10.1063/1.5002086.

PMID:
29117698
2.

Joint NDT image restoration and segmentation using Gauss-Markov-Potts prior models and variational Bayesian computation.

Ayasso H, Mohammad-Djafari A.

IEEE Trans Image Process. 2010 Sep;19(9):2265-77. doi: 10.1109/TIP.2010.2047902. Epub 2010 Apr 8.

PMID:
20378473
3.

Variational free energy and the Laplace approximation.

Friston K, Mattout J, Trujillo-Barreto N, Ashburner J, Penny W.

Neuroimage. 2007 Jan 1;34(1):220-34. Epub 2006 Oct 20.

PMID:
17055746
4.

A variational approach to niche construction.

Constant A, Ramstead MJD, Veissière SPL, Campbell JO, Friston KJ.

J R Soc Interface. 2018 Apr;15(141). pii: 20170685. doi: 10.1098/rsif.2017.0685. Review.

5.

Variational method for estimating the rate of convergence of Markov-chain Monte Carlo algorithms.

Casey FP, Waterfall JJ, Gutenkunst RN, Myers CR, Sethna JP.

Phys Rev E Stat Nonlin Soft Matter Phys. 2008 Oct;78(4 Pt 2):046704. Epub 2008 Oct 20.

PMID:
18999558
6.

Feynman's clock, a new variational principle, and parallel-in-time quantum dynamics.

McClean JR, Parkhill JA, Aspuru-Guzik A.

Proc Natl Acad Sci U S A. 2013 Oct 8;110(41):E3901-9. doi: 10.1073/pnas.1308069110. Epub 2013 Sep 23.

7.

Variational cross-validation of slow dynamical modes in molecular kinetics.

McGibbon RT, Pande VS.

J Chem Phys. 2015 Mar 28;142(12):124105. doi: 10.1063/1.4916292.

8.

Variational tensor approach for approximating the rare-event kinetics of macromolecular systems.

Nüske F, Schneider R, Vitalini F, Noé F.

J Chem Phys. 2016 Feb 7;144(5):054105. doi: 10.1063/1.4940774.

PMID:
26851906
9.

Commute Maps: Separating Slowly Mixing Molecular Configurations for Kinetic Modeling.

Noé F, Banisch R, Clementi C.

J Chem Theory Comput. 2016 Nov 8;12(11):5620-5630. Epub 2016 Oct 24.

PMID:
27696838
10.

Variational principle in dynamics of a vortex filament.

Berdichevsky VL.

Phys Rev E Stat Nonlin Soft Matter Phys. 2008 Sep;78(3 Pt 2):036304. Epub 2008 Sep 5.

PMID:
18851140
11.

Molecular Dynamics-Markov State Model of Protein Ligand Binding and Allostery in CRIB-PDZ: Conformational Selection and Induced Fit.

Thayer KM, Lakhani B, Beveridge DL.

J Phys Chem B. 2017 Jun 8;121(22):5509-5514. doi: 10.1021/acs.jpcb.7b02083. Epub 2017 May 25.

PMID:
28489401
12.

Variational Approach to Molecular Kinetics.

Nüske F, Keller BG, Pérez-Hernández G, Mey AS, Noé F.

J Chem Theory Comput. 2014 Apr 8;10(4):1739-52. doi: 10.1021/ct4009156. Epub 2014 Mar 6.

PMID:
26580382
13.

Elucidation of the conformational dynamics of multi-body systems by construction of Markov state models.

Zhu L, Sheong FK, Zeng X, Huang X.

Phys Chem Chem Phys. 2016 Nov 9;18(44):30228-30235.

PMID:
27314275
14.

Functional regression via variational Bayes.

Goldsmith J, Wand MP, Crainiceanu C.

Electron J Stat. 2011 Jan 1;5:572-602.

15.
16.

Automatic state partitioning for multibody systems (APM): an efficient algorithm for constructing Markov state models to elucidate conformational dynamics of multibody systems.

Sheong FK, Silva DA, Meng L, Zhao Y, Huang X.

J Chem Theory Comput. 2015 Jan 13;11(1):17-27. doi: 10.1021/ct5007168. Epub 2014 Dec 23.

PMID:
26574199
17.

Efficient variational Bayesian approximation method based on subspace optimization.

Zheng Y, Fraysse A, Rodet T.

IEEE Trans Image Process. 2015 Feb;24(2):681-93. doi: 10.1109/TIP.2014.2383321. Epub 2014 Dec 18.

PMID:
25532179
18.

Identification of slow molecular order parameters for Markov model construction.

Pérez-Hernández G, Paul F, Giorgino T, De Fabritiis G, Noé F.

J Chem Phys. 2013 Jul 7;139(1):015102. doi: 10.1063/1.4811489.

PMID:
23822324
19.

A Bayesian nonparametric approach for uncovering rat hippocampal population codes during spatial navigation.

Linderman SW, Johnson MJ, Wilson MA, Chen Z.

J Neurosci Methods. 2016 Apr 1;263:36-47. doi: 10.1016/j.jneumeth.2016.01.022. Epub 2016 Feb 5.

20.

Optimized parameter selection reveals trends in Markov state models for protein folding.

Husic BE, McGibbon RT, Sultan MM, Pande VS.

J Chem Phys. 2016 Nov 21;145(19):194103.

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