Related Articles tICA-Metadynamics: Accelerating Metadynamics by using kinetically selected collective variables. J Chem Theory Comput. 2017 Apr 06;: Authors: M Sultan M, Pande VS Abstract Metadynamics is a powerful enhanced…
Read moreRelated Articles Markov modeling reveals novel intracellular modulation of the human TREK-2 selectivity filter. Sci Rep. 2017 Apr 04;7(1):632 Authors: Harrigan MP, McKiernan KA, Shanmugasundaram V, Denny RA, Pande VS…
Read moreRelated Articles Computationally Discovered Potentiating Role of Glycans on NMDA Receptors. Sci Rep. 2017 Apr 05;7:44578 Authors: Sinitskiy AV, Stanley NH, Hackos DH, Hanson JE, Sellers BD, Pande VS Abstract…
Read moreAllosteric sodium in the helix bundle of a G protein-coupled receptor (GPCR) can modulate the receptor activation on the intracellular side. This phenomenon has confounded the GPCR community for decades. In this work, we present a theoretical model that reveals the mechanism of the allosteric modulation induced by sodium in the δ-opioid receptor. We found that the allosteric sodium ion exploits a distinct conformation of the key residue Trp2746.48 to propagate the modulation to helices 5 and 6…
Read moreWe 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…
Read moreIn 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 moreThe 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 moreWe 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 moreStanford IT managed to finish their work earlier than expected. Stats should be back up and operating normally.
Read moreThe stats server will be down between December 7th and the 9th. Points will not be accessible during this time, but will still be accruing.
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