Out with the old psummary, reminder of the new
Our projects page is a key way for donors to see the most up to date information about what is running on Folding@home. About a year and a half ago…
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Ensembler: Enabling High-Throughput Molecular Simulations at the Superfamily Scale.
PLoS Comput Biol. 2016 Jun 23;12(6):e1004728. doi: 10.1371/journal.pcbi.1004728. eCollection 2016. Parton DL, Grinaway PB, Hanson SM, Beauchamp KA, Chodera JD. The rapidly expanding body of available genomic and protein…
Read moreEnsembler: Enabling High-Throughput Molecular Simulations at the Superfamily Scale
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 moreWhere can I see more detail about what's going on in FAH?
For 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 moreClosing in on 100 Petaflops
It’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 moreMarkov State Models and tICA Reveal a Nonnative Folding Nucleus in Simulations of NuG2.
Biophys 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…
Read moreConformational heterogeneity of the calmodulin binding interface.
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 morePlanned server outage 2/28
The 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…
Read moreUsing Kinetic Network Models To Probe Non-Native Salt-Bridge Effects on α-Helix Folding.
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 moreNew paper on non-native salt-bridge effects on folding
Saltâbridges 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…
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