Issues with FahCore21
We’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…
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mTOR: Projects 10491-10499
In 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 moreMDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories.
Biophys 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 moreHeat dissipation guides activation in signaling proteins.
Proc 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 moreEfficient maximum likelihood parameterization of continuous-time Markov processes.
J 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…
Read moreUnited polarizable multipole water model for molecular mechanics simulation.
J Chem Phys. 2015 Jul 7;143(1):014504. doi: 10.1063/1.4923338. Qi R, Wang LP, Wang Q, Pande VS, Ren P We report the development of a united AMOEBA (uAMOEBA) polarizable water model,…
Read moreOpenMM: A Hardware Independent Framework for Molecular Simulations.
Comput Sci Eng. 2015 Jul 1;12(4):34-39. Eastman P, Pande VS The wide diversity of computer architectures today requires a new approach to software development. OpenMM is a framework for molecular…
Read moreA network of molecular switches controls the activation of the two-component response regulator NtrC.
Nat Commun. 2015 Jun 15;6:7283. doi: 10.1038/ncomms8283. Vanatta DK, Shukla D, Lawrenz M, Pande VS Recent successes in simulating protein structure and folding dynamics have demonstrated the power of molecular…
Read moreElucidating Ligand-Modulated Conformational Landscape of GPCRs Using Cloud-Computing Approaches.
Methods Enzymol. 2015;557:551-72. doi: 10.1016/bs.mie.2014.12.007. Epub 2015 Mar 24. Shukla D, Lawrenz M, Pande VS. G-protein-coupled receptors (GPCRs) are a versatile family of membrane-bound signaling proteins. Despite the recent successes…
Read moreVariational cross-validation of slow dynamical modes in molecular kinetics.
J Chem Phys. 2015 Mar 28;142(12):124105. doi: 10.1063/1.4916292. McGibbon RT, Pande VS Markov state models are a widely used method for approximating the eigenspectrum of the molecular dynamics propagator, yielding…
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