Search Results - "Pande, S"

Variational cross-validation of slow dynamical modes in molecular kinetics by McGibbon, Robert T, Pande, Vijay S

“…Markov state models are a widely used method for approximating the eigenspectrum of the molecular dynamics propagator, yielding insight into the long-timescale…”
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Building Force Fields: An Automatic, Systematic, and Reproducible Approach by Wang, Lee-Ping, Martinez, Todd J, Pande, Vijay S

“…The development of accurate molecular mechanics force fields is a significant challenge that must be addressed for the continued success of molecular…”
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Activation pathway of Src kinase reveals intermediate states as targets for drug design by Shukla, Diwakar, Meng, Yilin, Roux, Benoît, Pande, Vijay S.

“…Unregulated activation of Src kinases leads to aberrant signalling, uncontrolled growth and differentiation of cancerous cells. Reaching a complete mechanistic…”
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OpenMM 7: Rapid development of high performance algorithms for molecular dynamics by Eastman, Peter, Swails, Jason, Chodera, John D, McGibbon, Robert T, Zhao, Yutong, Beauchamp, Kyle A, Wang, Lee-Ping, Simmonett, Andrew C, Harrigan, Matthew P, Stern, Chaya D, Wiewiora, Rafal P, Brooks, Bernard R, Pande, Vijay S

“…OpenMM is a molecular dynamics simulation toolkit with a unique focus on extensibility. It allows users to easily add new features, including forces with novel…”
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To milliseconds and beyond: challenges in the simulation of protein folding by Lane, Thomas J, Shukla, Diwakar, Beauchamp, Kyle A, Pande, Vijay S

“…► Millisecond simulations. ► Hardware and software advances. ► Simulation to understanding. Quantitatively accurate all-atom molecular dynamics (MD)…”
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MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories by McGibbon, Robert T., Beauchamp, Kyle A., Harrigan, Matthew P., Klein, Christoph, Swails, Jason M., Hernández, Carlos X., Schwantes, Christian R., Wang, Lee-Ping, Lane, Thomas J., Pande, Vijay S.

“…As molecular dynamics (MD) simulations continue to evolve into powerful computational tools for studying complex biomolecular systems, the necessity of…”
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CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field by Lee, Jumin, Cheng, Xi, Swails, Jason M, Yeom, Min Sun, Eastman, Peter K, Lemkul, Justin A, Wei, Shuai, Buckner, Joshua, Jeong, Jong Cheol, Qi, Yifei, Jo, Sunhwan, Pande, Vijay S, Case, David A, Brooks, Charles L, MacKerell, Alexander D, Klauda, Jeffery B, Im, Wonpil

“…Proper treatment of nonbonded interactions is essential for the accuracy of molecular dynamics (MD) simulations, especially in studies of lipid bilayers. The…”
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MSMBuilder: Statistical Models for Biomolecular Dynamics by Harrigan, Matthew P., Sultan, Mohammad M., Hernández, Carlos X., Husic, Brooke E., Eastman, Peter, Schwantes, Christian R., Beauchamp, Kyle A., McGibbon, Robert T., Pande, Vijay S.

“…MSMBuilder is a software package for building statistical models of high-dimensional time-series data. It is designed with a particular focus on the analysis…”
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Building a More Predictive Protein Force Field: A Systematic and Reproducible Route to AMBER-FB15 by Wang, Lee-Ping, McKiernan, Keri A, Gomes, Joseph, Beauchamp, Kyle A, Head-Gordon, Teresa, Rice, Julia E, Swope, William C, Martínez, Todd J, Pande, Vijay S

“…The increasing availability of high-quality experimental data and first-principles calculations creates opportunities for developing more accurate empirical…”
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Towards simple kinetic models of functional dynamics for a kinase subfamily by Sultan, Mohammad M., Kiss, Gert, Pande, Vijay S.

“…Kinases are ubiquitous enzymes involved in the regulation of critical cellular pathways. However, in silico modelling of the conformational ensembles of these…”
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Transferable Neural Networks for Enhanced Sampling of Protein Dynamics by Sultan, Mohammad M, Wayment-Steele, Hannah K, Pande, Vijay S

“…Variational autoencoder frameworks have demonstrated success in reducing complex nonlinear dynamics in molecular simulation to a single nonlinear embedding. In…”
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Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways by Kohlhoff, Kai J., Shukla, Diwakar, Lawrenz, Morgan, Bowman, Gregory R., Konerding, David E., Belov, Dan, Altman, Russ B., Pande, Vijay S.

“…Simulations can provide tremendous insight into the atomistic details of biological mechanisms, but micro- to millisecond timescales are historically only…”
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Are Protein Force Fields Getting Better? A Systematic Benchmark on 524 Diverse NMR Measurements by Beauchamp, Kyle A, Lin, Yu-Shan, Das, Rhiju, Pande, Vijay S

“…Recent hardware and software advances have enabled simulation studies of protein systems on biophysically relevant time scales, often revealing the need for…”
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Revised Parameters for the AMOEBA Polarizable Atomic Multipole Water Model by Laury, Marie L, Wang, Lee-Ping, Pande, Vijay S, Head-Gordon, Teresa, Ponder, Jay W

“…A set of improved parameters for the AMOEBA polarizable atomic multipole water model is developed. An automated procedure, ForceBalance, is used to adjust…”
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Molecular Simulation of ab Initio Protein Folding for a Millisecond Folder NTL9(1−39) by Voelz, Vincent A, Bowman, Gregory R, Beauchamp, Kyle, Pande, Vijay S

“…To date, the slowest-folding proteins folded ab initio by all-atom molecular dynamics simulations have had folding times in the range of nanoseconds to…”
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PotentialNet for Molecular Property Prediction by Feinberg, Evan N, Sur, Debnil, Wu, Zhenqin, Husic, Brooke E, Mai, Huanghao, Li, Yang, Sun, Saisai, Yang, Jianyi, Ramsundar, Bharath, Pande, Vijay S

“…The arc of drug discovery entails a multiparameter optimization problem spanning vast length scales. The key parameters range from solubility (angstroms) to…”
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Conformational heterogeneity of the calmodulin binding interface by Shukla, Diwakar, Peck, Ariana, Pande, Vijay S.

“…Calmodulin (CaM) is a ubiquitous Ca 2+ sensor and a crucial signalling hub in many pathways aberrantly activated in disease. However, the mechanistic basis of…”
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Nanomechanics of Hall–Petch relationship in nanocrystalline materials by Pande, C.S., Cooper, K.P.

“…Classical Hall–Petch relation for large grained polycrystals is usually derived using the model of dislocation pile-up first investigated mathematically by…”
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Estimation of scallop height in freeform surface CNC Machining by Kukreja, Aman, Pande, S. S.

“…Scallop height is primarily used to assess the quality of complex freeform surface parts manufactured on multi-axis computer numerical control (CNC) machines…”
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Exploring the Helix-Coil Transition via All-Atom Equilibrium Ensemble Simulations by Sorin, Eric J., Pande, Vijay S.

“…The ensemble folding of two 21-residue α-helical peptides has been studied using all-atom simulations under several variants of the AMBER potential in explicit…”
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