Continued issues with Nvidia drivers
We are working together with Nvidia on an updated CUDA version of the OpenMM core to solve the issues with Nvidia drivers and to create a sustainable solution that will…
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New paper: predicting how mutations perturb folding
In a new article published in the Journal of Chemical Theory and Computation, researchers from the Voelz Lab address an important challenge for molecular simulation: how to efficiently predict the effects…
Read moreStats down, the team is on it
The stats server is down right now and we’re looking at it.  Our main IT support is out for the holidays so the time to get it back up may…
Read moreA Maximum-Caliber Approach to Predicting Perturbed Folding Kinetics Due to Mutations.
We present a maximum-caliber method for inferring transition rates of a Markov state model (MSM) with perturbed equilibrium populations given estimates of state populations and rates for an unperturbed MSM. It is similar in spirit to previous approaches, but given the inclusion of prior information, it is more robust and simple to implement. We examine its performance in simple biased diffusion models of kinetics and then apply the method to predicting changes in folding rates for several high…
Read moreStats back online!
Stanford IT managed to finish their work earlier than expected. Stats should be back up and operating normally.
Read moreStats Down for Scheduled Maintenance until 12/9
The stats server will be down between December 7th and the 9th. Points will not be accessible during this time, but will still be accruing.
Read moreDefining NADH-Driven Allostery Regulating Apoptosis-Inducing Factor.
Apoptosis-inducing factor (AIF) is critical for mitochondrial respiratory complex biogenesis and for mediating necroptotic parthanatos; these functions are seemingly regulated by enigmatic allosteric switching driven by NADH charge-transfer complex (CTC) formation. Here, we define molecular pathways linking AIF’s active site to allosteric switching regions by characterizing dimer-permissive mutants using small-angle X-ray scattering (SAXS) and crystallography and by probing AIF-CTC communicati…
Read moreTraining and Validation of a Liquid-Crystalline Phospholipid Bilayer Force Field.
Related Articles Training and Validation of a Liquid-Crystalline Phospholipid Bilayer Force Field. J Chem Theory Comput. 2016 Dec 13;12(12):5960-5967 Authors: McKiernan KA, Wang LP, Pande VS Abstract We present a…
Read moreMeasuring experimental cyclohexane-water distribution coefficients for the SAMPL5 challenge.
Small molecule distribution coefficients between immiscible nonaqueuous and aqueous phases-such as cyclohexane and water-measure the degree to which small molecules prefer one phase over another at a given pH. As distribution coefficients capture both thermodynamic effects (the free energy of transfer between phases) and chemical effects (protonation state and tautomer effects in aqueous solution), they provide an exacting test of the thermodynamic and chemical accuracy of physical models with…
Read moreUsing F@H to “Drug the Undruggable”
In Project 10490, the Chodera lab is studying a small protein called KRAS, which forms a key link in growth signaling and cancer. This gene is something like a molecular…
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