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Author: Tor Raswill

Markov modeling reveals novel intracellular modulation of the human TREK-2 selectivity filter.

April 5, 2017 by Tor Raswill

Related 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…

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Computationally Discovered Potentiating Role of Glycans on NMDA Receptors.

April 5, 2017 by Tor Raswill

Related 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…

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MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories.

October 21, 2015 by Tor Raswill

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…

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Heat dissipation guides activation in signaling proteins.

October 21, 2015 by Tor Raswill

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…

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Efficient maximum likelihood parameterization of continuous-time Markov processes.

October 21, 2015 by Tor Raswill

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…

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United polarizable multipole water model for molecular mechanics simulation.

October 21, 2015 by Tor Raswill

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,…

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OpenMM: A Hardware Independent Framework for Molecular Simulations.

October 21, 2015 by Tor Raswill

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…

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A network of molecular switches controls the activation of the two-component response regulator NtrC.

October 21, 2015 by Tor Raswill

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…

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Elucidating Ligand-Modulated Conformational Landscape of GPCRs Using Cloud-Computing Approaches.

October 21, 2015 by Tor Raswill

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…

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Variational cross-validation of slow dynamical modes in molecular kinetics.

October 21, 2015 by Tor Raswill

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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