D. L. Ensign and V. S. Pande. Biophysical Journal 96 L53-55 (2009) ABSTRACT. We describe molecular dynamics simulations resulting in the folding the Fip35 Hpin1 WW domain. The simulations were…
Read moreM. S. Friedrichs, P. Eastman, V. Vaidyanathan, M. Houston, S. LeGrand, A. L. Beberg, D. L. Ensign, C. M. Bruns, V. S. Pande. J. Comp. Chem., (2009) SUMMARY. This paper…
Read moreNicholas W. Kelley, Xuhui Huang, Stephen Tam, Christoph Spiess, Judith Frydman and Vijay S. Pande. Journal of Molecular Biology (2009) SUMMARY. The aggregation of the Huntingtin (Htt) protein has been…
Read morePeter M. Kasson and Vijay S. Pande. Pacific Symposium on Biocomputing 14:492-503(2009). SUMMARY. The influenza hemagglutinin protein performs several important functions, including attaching the virus to cells it will infect…
Read moreEdgar Luttmann, Daniel L. Ensign, Vishal Vaidyanathan, Mike Houston, Noam Rimon, Jeppe Øland, Guha Jayachandran, Mark Friedrichs, Vijay S. Pande. Journal of Computational Chemistry (2009) SUMMARY. In this paper, we…
Read morePaula M. Petrone, Christopher D. Snow, Del Lucent, and Vijay S. Pande Proceedings of the National Academy of Sciences, USA 2008 SUMMARY The ribosome is a fascinating molecular machine, responsible…
Read moreNicholas W. Kelley, V. Vishal, Grant A. Krafft, and Vijay S. Pande J. Chem. Phys. 129, 214707 (2008); DOI:10.1063/1.3010881 SUMMARY. Abeta misfolding and aggregation is believed to be the cause…
Read moreGregory R. Bowman, Xuhui Huang, Yuan Yao, Jian Sun, Gunnar Carlsson, Leonidas J. Guibas, and Vijay S. Pande J. Am. Chem. Soc., 130 (30), 9676–9678, 2008 ABSTRACT. Hairpins are a…
Read moreXuhui Huang,Gregory R. Bowman,and Vijay S. Pande J Chem Phys. 2008 May 28;128(20):205106. ABSTRACT.We have implemented the serial replica exchange method (SREM) and simulated tempering (ST) enhanced sampling algorithms in…
Read moreNina Singhal Heinrichs and Vijay S. Pande. Journal of Chemical Physics (2007) SUMMARY. This paper lays out how one can revamp FAH calculations to make them considerably more efficient, perhaps…
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