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News

Solvation free energies of amino acid side chain analogs for common molecular mechanics water models.

October 4, 2005 by Viktor

Michael R. Shirts & Vijay S. Pande. Journal of Chemical Physics (2005) SUMMARY: This paper is a test of our methods for free energy calculation — critical to our computational…

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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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Parkinson’s Disease

September 19, 2005 by Folding@Home

We started a pilot study on Parkinson’s Disease, and started to look for further funding to continue our work in the area.

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Osteogenesis Imperfecta

September 19, 2005 by Folding@Home

Our first work on collagen mutations connected to Osteogenesis Imperfecta was accepted for publication.

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