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News

Can conformational change be described by only a few normal modes?

October 4, 2006 by Viktor

Paula Petrone and Vijay S. Pande. Biophysical Journal (2006) SUMMARY: In allosteric regulation, protein activity is altered when ligand binding (or unbinding) causes changes in the protein conformation. Little is…

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Huntington’s Disease

September 19, 2006 by Folding@Home

The first papers on Folding@home results in regards to Huntington’s Disease were submitted.

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Submitting first paper

September 15, 2006 by Folding@Home

We are currently in the process of submitting our first paper on FAH results.

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First paper submitted for peer review

September 15, 2006 by Folding@Home

We have submitted our first paper for peer review and we’re working on the next 2 paper right now. We’re very excited about the results!

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p53 presentation

September 15, 2006 by Folding@Home

FAH researcher Dr. Lillian Chong presented her work on p53 at a lecture at several US Universities.

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How large is alpha-helix in solution? Studies of the radii of gyration of helical peptides by SAXS and MD.

October 4, 2005 by Viktor

Bojan Zagrovic, Guha Jayachandran, Ian S. Millett, Sebastian Doniach and Vijay S. Pande. Journal of Molecular Biology (2005) SUMMARY: Direct comparisons are made between Folding@home simulations and experimental measurements (SAXS)…

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Error Analysis in Markovian State Models for protein folding.

October 4, 2005 by Viktor

Nina Singhal and Vijay S. Pande. Journal of Chemical Physics (2005) SUMMARY: We validate the new Markovian State Model (MSM) for describing protein dynamics, and show how to efficiently calculate…

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Direct calculation of the binding free energies of FKBP ligands using the Fujitsu BioServer massively parallel computer.

October 4, 2005 by Viktor

Hideaki Fujutani, Yoshiaki Tanida, Masakatsu Ito, Guha Jayachandran, Christopher D. Snow, Michael R. Shirts, Eric J. Sorin, and Vijay S. Pande Journal of Chemical Physics (2005) SUMMARY: Drug design calculations…

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A New Set of Molecular Mechanics Parameters for Hydroxyproline and Its Use in Molecular Dynamics Simulations of Collagen-Like Peptides.

October 4, 2005 by Viktor

Sanghyun Park, Randall J. Radmer, Teri E. Klein, and Vijay S. Pande. Journal of Computational Chemistry (2005) SUMMARY: Simulation of the collagen triple helix has been given less attention than…

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Comparison of efficiency and bias of free energies computed by exponential averaging, the Bennett acceptance ratio, and thermodynamic integration.

October 4, 2005 by Viktor

Michael R. Shirts & Vijay S. Pande. Journal of Chemical Physics (2005) SUMMARY: We test new methods for free energy calculations — relevant for our computational drug design methodology. We…

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