The rapidly expanding body of available genomic and protein structural data provides a rich resource for understanding protein dynamics with biomolecular simulation. While computational infrastructure has grown rapidly, simulations on an omics scale are not yet widespread, primarily because software infrastructure to enable simulations at this scale has not kept …
Read moreFor those new to FAH, here’s a reminder for where the nitty gritty details can be found if people are interested to learn more than what’s on our web site.…
Read moreIt’s been a while since we updated the FLOP per GPU report (since Tue, 26 Feb 2013 in fact).  A lot of progress has been made in 3+ years in GPU-land.…
Read moreBiophys J. 2016 Apr 26;110(8):1716-9. doi: 10.1016/j.bpj.2016.03.026. Schwantes CR, Shukla D, Pande VS After reanalyzing simulations of NuG2-a designed mutant of protein G-generated by Lindorff-Larsen et al. with time structure-based independent…
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Nat Commun. 2016 Apr 4;7:10910. doi: 10.1038/ncomms10910. Shukla D ,Peck A , Pande VS Finally, our model predicts a novel binding interface that is well-populated in the Ca(2+)-bound regime and, thus, a…
Read moreThe Stanford networking team will be upgrading some infrastructure this coming Sunday, February 28, 2016, from 12AM – 4AM. This work will be partially  disruptive to where some key FAH content is…
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J Phys Chem B. 2016 Feb 11;120(5):926-35. doi: 10.1021/acs.jpcb.5b11767. Epub 2016 Feb 1. Zhou G, Voelz VA. Salt-bridge interactions play an important role in stabilizing many protein structures, and have…
Read moreSaltâbridges are electrostatic interactions between positively charged residue side chains (like arginine or lysine) and negatively-charged side chains (like aspartic and glutamic acids). They play an important role in stabilizing…
Read morePeptoids (N-substituted oligoglycines) are biomimetic polymers that can fold into a variety of unique structural scaffolds. Peptoid helices, which result from the incorporation of bulky chiral side chains, are a key peptoid structural motif whose formation has not yet been accurately modeled in molecular simulations. Here, we report that a simple modification of the backbone Ï-angle potential in GAFF is able to produce well-folded cis-amide helices of (S)-N-(1-phenylethyl)glycine (Nspe), consi…
Read moreMolecular dynamics simulations are a powerful means of understanding conformational changes. However, it is still difficult to simulate biologically relevant time scales without the use of specialized supercomputers. Here, we introduce a goal-oriented sampling method, called fluctuation amplification of specific traits (FAST), for extending the capabilities of commodity hardware. This algorithm rapidly searches conformational space for structures with desired properties by balancing trade-offs…
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