First paper submitted for peer review
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
FAH researcher Dr. Lillian Chong presented her work on p53 at a lecture at several US Universities.
Read moreHow large is alpha-helix in solution? Studies of the radii of gyration of helical peptides by SAXS and MD.
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)…
Read moreError Analysis in Markovian State Models for protein folding.
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…
Read moreDirect calculation of the binding free energies of FKBP ligands using the Fujitsu BioServer massively parallel computer.
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…
Read moreA New Set of Molecular Mechanics Parameters for Hydroxyproline and Its Use in Molecular Dynamics Simulations of Collagen-Like Peptides.
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…
Read moreComparison of efficiency and bias of free energies computed by exponential averaging, the Bennett acceptance ratio, and thermodynamic integration.
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…
Read moreSolvation free energies of amino acid side chain analogs for common molecular mechanics water models.
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…
Read moreFoldamer dynamics expressed via Markov state models. I. Explicit solvent molecular-dynamics simulations in acetonitrile, chloroform, methanol, and water.
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…
Read moreFoldamer dynamics expressed via Markov state models. II. State space decomposition.
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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