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Author: Viktor

Foldamer dynamics expressed via Markov state models. I. Explicit solvent molecular-dynamics simulations in acetonitrile, chloroform, methanol, and water.

October 4, 2005 by Viktor

Sidney Elmer, Sanghyun Park, & Vijay S. Pande. Journal of Chemical Physics (2005) SUMMARY: Here, we lay out some of the first applications of a new method for future FAH…

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Foldamer dynamics expressed via Markov state models. II. State space decomposition.

October 4, 2005 by Viktor

Sidney Elmer, Sanghyun Park, & Vijay S. Pande. Journal of Chemical Physics (2005) SUMMARY: Here, we lay out some new methodology for simulation for future FAH calculations. This new method,…

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Unusual compactness of a polyproline type II structure.

October 4, 2005 by Viktor

Bojan Zagrovic, Jan Lipfert, Eric J. Sorin, Ian S. Millett, Wilfred F. van Gunsteren, Sebastian Doniach & Vijay S. Pande. Proceedings of the National Academy of Sciences (2005) SUMMARY: This…

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How well can simulation predict protein folding kinetics and thermodynamics?

October 4, 2005 by Viktor

Christopher D. Snow, Eric J. Sorin, Young Min Rhee, and Vijay S. Pande. Annual Review of Biophysics & Biomolecular Structure (2005) SUMMARY: Rather than reporting new data from the Folding@home…

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Empirical Force-Field Assessment: The Interplay Between Backbone Torsions and Noncovalent Term Scaling.

October 4, 2005 by Viktor

Eric J. Sorin and Vijay S. Pande. Journal of Computational Chemistry (2005) SUMMARY: How do the results of peptide simulations change with slight variations to the models employed? Here we…

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Exploring the Helix-Coil Transition via All-atom Equilibrium Ensemble Simulations.

October 4, 2005 by Viktor

Eric J. Sorin and Vijay S. Pande. Biophysical Journal (2005) SUMMARY: How good are our models for folding? This question is important to address in order to understand the usefulness…

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Does Water Play a Structural Role in the Folding of Small Nucleic Acids?

October 4, 2005 by Viktor

Eric J. Sorin, Young Min Rhee, and Vijay S. Pande. Biophysical Journal (2005) SUMMARY: While previous studies on the folding of nucleic acid hairpins have employed simplified models of either…

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Dimerization of the p53 Oligomerization Domain: Identification of a Folding Nucleus by Molecular Dynamics Simulations.

October 4, 2004 by Viktor

Lillian T. Chong, Christopher D. Snow, Young Min Rhee, and Vijay S. Pande. Journal of Molecular Biology (2005) SUMMARY: Roughly half of all known cancers result from mutations in p53.…

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

October 4, 2004 by Viktor

Nina Singhal, Christopher D. Snow, and Vijay S. Pande. Journal of Chemical Physics (2004) SUMMARY: How can Folding@home use thousands to millions of CPUs to efficiently simulate long timescale biomolecular…

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Simulations of the role of water in the protein-folding mechanism.

October 4, 2004 by Viktor

Young Min Rhee, Eric J. Sorin, Guha Jayachandran, Erik Lindahl, & Vijay S Pande. Proceedings of the National Academy of Sciences (2004) ABSTRACT: There are many unresolved questions regarding the…

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