Closing 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.…
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Markov 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
Salt−bridges 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 moreInsights into Peptoid Helix Folding Cooperativity from an Improved Backbone Potential.
Peptoids (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 φ-angle potential in GAFF is able to produce well-folded cis-amide helices of (S)-N-(1-phenylethyl)glycine (Nspe), consi…
Read moreFAST Conformational Searches by Balancing Exploration/Exploitation Trade-Offs.
Molecular 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…
Read moreFAH's achievements in 2015, with a glimpse into 2016
We’re reaching the end of 2015 and as in previous years, I’d like to summarize for donors what Folding@home (FAH) has done in 2015 and where we’re going. In general,…
Read moreNew paper on peptoid helix folding from the Voelz Lab
Nature relies on the remarkable folding properties of proteins and nucleic acids to perform vital chemical work. Not surprisingly, synthetic chemists have long set their sights on developing non-natural molecules—called…
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