J Phys Chem B. 2015 Jul 23;119(29):9423-37. doi: 10.1021/jp510896n. Epub 2015 Feb 26.Laury ML1, Wang LP2, Pande VS2, Head-Gordon T3, Ponder JW1. A set of improved parameters for the AMOEBA…
Read moreAcc Chem Res. 2015 Feb 17;48(2):414-22 Authors: Shukla D, Hernández CX, Weber JK, Pande VS. Protein function is inextricably linked to protein dynamics. As we move from a static structural…
Read moreLawrenz M1, Shukla D2, Pande VS. Sci Rep. 2015; 5: 7918. We describe an innovative protocol for ab initio prediction of ligand crystallographic binding poses and highly effective analysis of…
Read moreD. Shukla, Y. L. Meng, B. Roux, and V. S. Pande. Nat Commun 5 (2014) Unregulated activation of Src kinases leads to aberrant signalling, uncontrolled growth and differentiation of cancerous…
Read moreR. T. McGibbon, C. R. Schwantes, and V. S. Pande. J Phys Chem B. 118 6475-81 (2014) Markov state models provide a powerful framework for the analysis of biomolecular conformation…
Read moreJ. K. Weber, R. L. Jack, C. R. Schwantes, and V. S. Pande. Biophys J. 107(4) 974-82 (2014). Developing an understanding of protein misfolding processes presents a crucial challenge for…
Read moreC. R. Baiz, Y.-S. Lin, C. S. Peng, K. A. Beauchamp, V. A. Voelz, V. S. Pande, and A. Tokmakoff. Biophysical Journal, 106 1359-1370 (2014) The folding mechanism of the…
Read moreK. J. Kohlhoff*, D. Shukla*, M. Lawrenz*, G. R. Bowman, D. E. Konerding, D. Belov, R, B. Altman, and V. S. Pande. Nature Chemistry 6 15-21 (2014) We applied methods developed and honed…
Read moreR. T. McGibbon and V. S. Pande. J. Chem. Theory Comput., DOI: 10.1021/ct400132h (2013) Building Markov State Models (MSMs) is at the heart of how FAH can take advantage of hundreds of thousands…
Read moreC. Schwantes and V. S. Pande. Journal of Computational and Theoretical Chemistry, in press (2013) A third paper in improved MSM designs, this paper shows how modern MSMs approaches can now pick…
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