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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…

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,…

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…

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…

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…

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…

J Phys Chem B. 2015 Jul 23;119(29):9423-37. doi: 10.1021/jp510896n. Epub 2015 Feb 26.Laury ML1, Wang LP2, Pande VS2, Head-Gordon T3, Ponder JW1. A set of improved parameters for the AMOEBA…

Acc Chem Res. 2015 Feb 17;48(2):414-22 Authors: Shukla D, Hernández CX, Weber JK, Pande VS. Protein function is inextricably linked to protein dynamics. As we move from a static structural…

Lawrenz M1, Shukla D2, Pande VS. Sci Rep. 2015; 5: 7918. We describe an innovative protocol for ab initio prediction of ligand crystallographic binding poses and highly effective analysis of…