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Transfer Learning from Markov Models Leads to Efficient Sampling of Related Systems.
Sultan MM, Pande VS. Sultan MM, et al. Among authors: pande vs. J Phys Chem B. 2018 May 31;122(21):5291-5299. doi: 10.1021/acs.jpcb.7b06896. Epub 2017 Oct 3. J Phys Chem B. 2018. PMID: 28938073
Solvent viscosity dependence of the folding rate of a small protein: distributed computing study.
Zagrovic B, Pande V. Zagrovic B, et al. J Comput Chem. 2003 Sep;24(12):1432-6. doi: 10.1002/jcc.10297. J Comput Chem. 2003. PMID: 12868108
Equilibrium free energies from nonequilibrium measurements using maximum-likelihood methods.
Shirts MR, Bair E, Hooker G, Pande VS. Shirts MR, et al. Among authors: pande vs. Phys Rev Lett. 2003 Oct 3;91(14):140601. doi: 10.1103/PhysRevLett.91.140601. Epub 2003 Oct 2. Phys Rev Lett. 2003. PMID: 14611511
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
Exploring the helix-coil transition via all-atom equilibrium ensemble simulations.
Sorin EJ, Pande VS. Sorin EJ, et al. Among authors: pande vs. Biophys J. 2005 Apr;88(4):2472-93. doi: 10.1529/biophysj.104.051938. Epub 2005 Jan 21. Biophys J. 2005. PMID: 15665128 Free PMC article.
Empirical force-field assessment: The interplay between backbone torsions and noncovalent term scaling.
Sorin EJ, Pande VS. Sorin EJ, et al. Among authors: pande vs. J Comput Chem. 2005 May;26(7):682-90. doi: 10.1002/jcc.20208. J Comput Chem. 2005. PMID: 15754305
Comparison of efficiency and bias of free energies computed by exponential averaging, the Bennett acceptance ratio, and thermodynamic integration.
Shirts MR, Pande VS. Shirts MR, et al. Among authors: pande vs. J Chem Phys. 2005 Apr 8;122(14):144107. doi: 10.1063/1.1873592. J Chem Phys. 2005. PMID: 15847516
A new set of molecular mechanics parameters for hydroxyproline and its use in molecular dynamics simulations of collagen-like peptides.
Park S, Radmer RJ, Klein TE, Pande VS. Park S, et al. Among authors: pande vs. J Comput Chem. 2005 Nov 30;26(15):1612-6. doi: 10.1002/jcc.20301. J Comput Chem. 2005. PMID: 16170799
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
Foldamer dynamics expressed via Markov state models. I. Explicit solvent molecular-dynamics simulations in acetonitrile, chloroform, methanol, and water.
Elmer SP, Park S, Pande VS. Elmer SP, et al. Among authors: pande vs. J Chem Phys. 2005 Sep 15;123(11):114902. doi: 10.1063/1.2001648. J Chem Phys. 2005. PMID: 16392592
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