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 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 φ-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…
Read moreWe’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 moreNature 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…
Read moreWe’ve discovered that the new FahCore_21 is producing more errors than we consider acceptable for some clients. Â The error rate seems to depend on several factors but most noticeable is…
Read moreIn projects 10491-10499, the Chodera lab takes a look at mTOR, a serine/threonine kinase. The MTOR gene was originally discovered in yeast in 1991 and named TOR1/2 because it was…
Read moreBiophys J. 2015 Oct 20;109(8):1528-32. doi: 10.1016/j.bpj.2015.08.015. McGibbon RT, Beauchamp KA, Harrigan MP, Klein C, Swails JM, Hernández CX, Schwantes CR, Wang LP, Lane TJ, Pande VS As molecular dynamics…
Read moreProc Natl Acad Sci U S A. 2015 Aug 18;112(33):10377-82. doi: 10.1073/pnas.1501804112. Epub 2015 Aug 3. Weber JK, Shukla D, Pande VS Life is fundamentally a nonequilibrium phenomenon. At the…
Read moreJ Chem Phys. 2015 Jul 21;143(3):034109. doi: 10.1063/1.4926516. McGibbon RT, Pande VS. Continuous-time Markov processes over finite state-spaces are widely used to model dynamical processes in many fields of natural…
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