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Journal of Chemical Theory and Computation|April 2, 2025
Improving pKa Predictions with Reparameterized Force Fields and Free Energy CalculationsCarter J Wilson, Vytautas Gapsys, Bert L de GrootJournal of Computational Chemistry|March 12, 2024
Resolving coupled pH titrations using alchemical free energy calculationsCarter J Wilson, Bert L de Groot, Vytautas GapsysJournal of Chemical Theory and Computation|October 11, 2023
Accurately Predicting Protein pKa Values Using Nonequilibrium AlchemyCarter J Wilson, Mikko Karttunen, Bert L de Groot, et al.Journal of Chemical Theory and Computation|November 11, 2017
Alchemical Free Energy Calculations for Nucleotide Mutations in Protein-DNA ComplexesVytautas Gapsys, Bert L de GrootElife|June 21, 2019
Comment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'Vytautas Gapsys, Bert L de GrootBiophysical Journal|January 22, 2013
Optimal superpositioning of flexible molecule ensemblesVytautas Gapsys, Bert L de GrootJournal of Chemical Information and Modeling|February 10, 2017
pmx Webserver: A User Friendly Interface for AlchemistryVytautas Gapsys, Bert L de GrootElife|August 20, 2020
On the importance of statistics in molecular simulations for thermodynamics, kinetics and simulation box sizeVytautas Gapsys, Bert L de GrootJournal of Chemical Theory and Computation|November 22, 2015
New Soft-Core Potential Function for Molecular Dynamics Based Alchemical Free Energy CalculationsVytautas Gapsys, Daniel Seeliger, Bert L de GrootJournal of Computer-Aided Molecular Design|October 24, 2013
Computational analysis of local membrane propertiesVytautas Gapsys, Bert L de Groot, Rodolfo BrionesPageof 21