Category: Papers

J. K. Weber, R. Jack, and V. S. Pande.  JACS, in press (2013) With all of our work in protein folding, we can step back and ask questions of what’s common, especially…

Lane TJ, Shukla D, Beauchamp KA, Pande VS. Current Opinion in Structural Biology (Feb 2013) The folding times accessible by simulation have increased exponentially over the past decade. Shown are…

Eastman P, Friedrichs MS, Chodera JD, Radmer RJ, Bruns CM, Ku JP, Beauchamp KA, Lane TJ, Wang LP, Shukla D, Tye T, Houston M, Stich T, Klein C, Shirts MR,…

Cronkite-Ratcliff B, Pande V. Bioinformatics. (Jan 2013) ABSTRACT. Markov state models (MSMs) for the study of biomolecule folding simulations have emerged as a powerful tool for computational study of folding…

Gu C, Chang HW, Maibaum L, Pande VS, Carlsson GE, Guibas LJ. BMC Bioinformatics, (Jan 2013) doi: 10.1186/1471-2105-14-S2-S8 SUMMARY. In this paper we have initiated an study to build Markov…

Markov state models (MSMs) have become a popular approach for investigating the conformational dynamics of proteins and other biomolecules. MSMs are typically built from numerous molecular dynamics simulations by dividing the sampled configurations into a large number of microstates based on geometric criteria. The resulting microstate model can then be coarse-gr…

Lin YS, Pande VS. Biophysical Journal (Dec 2012) SUMMARY. This details some new results from Folding@home on Alzheimer’s Disease. ABSTRACT. Amyloid beta (Aβ) peptide plays an important role in Alzheimer’s…

Ring AM, Lin JX, Feng D, Mitra S, Rickert M, Bowman GR, Pande VS, Li P, Moraga I, Spolski R, Ozkan E, Leonard WJ, Garcia KC. Natural Immunology (Dec 2012)…

Walker JR, Novick PA, Parsons WH, McGregor M, Zablocki J, Pande VS, Du Bois J. Proceedings of the National Academy of Sciences, USA (Dec 2012) SUMMARY. Here we use molecular…

Beauchamp KA, McGibbon R, Lin YS, Pande VS. Proceedings of the National Academy of Sciences, USA (Oct 2012) SUMMARY. Markov State Models (MSMs) have been very helpful in analyzing protein…