Pande VS - Search Results

1

Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics.

Chodera JD, Singhal N, Pande VS, Dill KA, Swope WC. Chodera JD, et al. Among authors: pande vs. J Chem Phys. 2007 Apr 21;126(15):155101. doi: 10.1063/1.2714538. J Chem Phys. 2007. PMID: 17461665

2

Bayesian comparison of Markov models of molecular dynamics with detailed balance constraint.

Bacallado S, Chodera JD, Pande V. Bacallado S, et al. J Chem Phys. 2009 Jul 28;131(4):045106. doi: 10.1063/1.3192309. J Chem Phys. 2009. PMID: 19655927 Free PMC article.

3

Using path sampling to build better Markovian state models: predicting the folding rate and mechanism of a tryptophan zipper beta hairpin.

Singhal N, Snow CD, Pande VS. Singhal N, et al. Among authors: pande vs. J Chem Phys. 2004 Jul 1;121(1):415-25. doi: 10.1063/1.1738647. J Chem Phys. 2004. PMID: 15260562

4

Error analysis and efficient sampling in Markovian state models for molecular dynamics.

Singhal N, Pande VS. Singhal N, et al. Among authors: pande vs. J Chem Phys. 2005 Nov 22;123(20):204909. doi: 10.1063/1.2116947. J Chem Phys. 2005. PMID: 16351319

5

Dynamical reweighting: improved estimates of dynamical properties from simulations at multiple temperatures.

Chodera JD, Swope WC, Noé F, Prinz JH, Shirts MR, Pande VS. Chodera JD, et al. Among authors: pande vs. J Chem Phys. 2011 Jun 28;134(24):244107. doi: 10.1063/1.3592152. J Chem Phys. 2011. PMID: 21721612 Free PMC article.

6

Optimal use of data in parallel tempering simulations for the construction of discrete-state Markov models of biomolecular dynamics.

Prinz JH, Chodera JD, Pande VS, Swope WC, Smith JC, Noé F. Prinz JH, et al. Among authors: pande vs. J Chem Phys. 2011 Jun 28;134(24):244108. doi: 10.1063/1.3592153. J Chem Phys. 2011. PMID: 21721613 Free PMC article.

7

Ensemble molecular dynamics yields submillisecond kinetics and intermediates of membrane fusion.

Kasson PM, Kelley NW, Singhal N, Vrljic M, Brunger AT, Pande VS. Kasson PM, et al. Among authors: pande vs. Proc Natl Acad Sci U S A. 2006 Aug 8;103(32):11916-21. doi: 10.1073/pnas.0601597103. Epub 2006 Jul 31. Proc Natl Acad Sci U S A. 2006. PMID: 16880392 Free PMC article.

8

Progress and challenges in the automated construction of Markov state models for full protein systems.

Bowman GR, Beauchamp KA, Boxer G, Pande VS. Bowman GR, et al. Among authors: pande vs. J Chem Phys. 2009 Sep 28;131(12):124101. doi: 10.1063/1.3216567. J Chem Phys. 2009. PMID: 19791846 Free PMC article.

9

Splitting probabilities as a test of reaction coordinate choice in single-molecule experiments.

Chodera JD, Pande VS. Chodera JD, et al. Among authors: pande vs. Phys Rev Lett. 2011 Aug 26;107(9):098102. doi: 10.1103/PhysRevLett.107.098102. Epub 2011 Aug 23. Phys Rev Lett. 2011. PMID: 21929272 Free PMC article.

10

Kinetic computational alanine scanning: application to p53 oligomerization.

Chong LT, Swope WC, Pitera JW, Pande VS. Chong LT, et al. Among authors: pande vs. J Mol Biol. 2006 Mar 31;357(3):1039-49. doi: 10.1016/j.jmb.2005.12.083. Epub 2006 Jan 17. J Mol Biol. 2006. PMID: 16457841

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