Planned maintenance complete, server room back online
Our planned maintenance is now complete and that server room is now back online. Â The stats update has recommenced.
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Stats manually turned off in preparation for early Tuesday morning shutdown
One of our primary server rooms will be shutdown for service tomorrow morning. Â Most of FAH will be operational, but we’re taking the stats update off line now so there…
Read moreLearning Kinetic Distance Metrics for Markov State Models of Protein Conformational Dynamics.
R. T. McGibbon and V. S. Pande.  J. Chem. Theory Comput., DOI: 10.1021/ct400132h (2013) Building Markov State Models (MSMs) is at the heart of how FAH can take advantage of hundreds of thousands…
Read moreImprovements in Markov State Model Construction Reveal Many Non-Native Interactions in the Folding of NTL9.
C. Schwantes and V. S. Pande.  Journal of Computational and Theoretical Chemistry, in press (2013) A third paper in improved MSM designs, this paper shows how modern MSMs approaches can now pick…
Read moreEmergence of Glass-like Behavior in Markov State Models of Protein Folding Dynamics.
J. K. Weber, R. Jack, and V. S. Pande.  JACS, in press (2013) With all of our work in protein folding, we can step back and ask questions of what’s common, especially…
Read moreTo milliseconds and beyond: challenges in the simulation of protein folding.
Lane TJ, Shukla D, Beauchamp KA, Pande VS. Current Opinion in Structural Biology (Feb 2013) The folding times accessible by simulation have increased exponentially over the past decade. Shown are…
Read moreOpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation.
Eastman P, Friedrichs MS, Chodera JD, Radmer RJ, Bruns CM, Ku JP, Beauchamp KA, Lane TJ, Wang LP, Shukla D, Tye T, Houston M, Stich T, Klein C, Shirts MR,…
Read moreMSMExplorer: Visualizing Markov State Models for Biomolecule Folding Simulations.
Cronkite-Ratcliff B, Pande V. Bioinformatics. (Jan 2013) ABSTRACT. Markov state models (MSMs) for the study of biomolecule folding simulations have emerged as a powerful tool for computational study of folding…
Read moreBuilding Markov state models with solvent dynamics
Gu C, Chang HW, Maibaum L, Pande VS, Carlsson GE, Guibas LJ. BMC Bioinformatics, (Jan 2013) doi: 10.1186/1471-2105-14-S2-S8 SUMMARY. In this paper we have initiated an study to build Markov…
Read morePlanned server room shutdown October 22 at 6am pacific time
One of our main server rooms is going through planned maintenance on Tuesday, October 22 starting at 6:00 AM pacific time.  The outage is expected to be less than one hour,…
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