Michael R. Shirts

16 papers Journal 16
YearRankTypeTitle / Venue / Authors
2024 J jnl
Parameterization of General Organic Polymers within the Open Force Field Framework.
J. Chem. Inf. Model.
Connor M. Davel, Timotej Bernat, Jeffrey R. Wagner, Michael R. Shirts
2024 J jnl
alchemlyb: the simple alchemistry library.
J. Open Source Softw.
Zhiyi Wu, David L. Dotson, Irfan Alibay, Bryce K. Allen, Mohammad Soroush Barhaghi, Jérôme Hénin, Thomas T. Joseph, Ian M. Kenney, Hyungro Lee, Haoxi Li, Victoria T. Lim, Shuai Liu, Domenico Marson, Pascal T. Merz, Alexander Schlaich, David L. Mobley, Michael R. Shirts, Oliver Beckstein
2022 J jnl
Bayesian-Inference-Driven Model Parametrization and Model Selection for 2CLJQ Fluid Models.
J. Chem. Inf. Model.
Owen Madin, Simon Boothroyd, Richard A. Messerly, Josh Fass, John D. Chodera, Michael R. Shirts
2022 J jnl
Identifying signatures of proteolytic stability and monomeric propensity in O-glycosylated insulin using molecular simulation.
J. Comput. Aided Mol. Des.
Wei-Tse Hsu, Dominique A. Ramirez, Tarek Sammakia, Zhongping Tan, Michael R. Shirts
2022 J jnl
physical_validation: A Python package to assess the physical validity of molecular simulation results.
J. Open Source Softw.
Pascal T. Merz, Wei-Tse Hsu, Matt W. Thompson, Simon Boothroyd, Chris C. Walker, Michael R. Shirts
2020 J jnl
Adaptive Ensemble Biomolecular Applications at Scale.
SN Comput. Sci.
Vivek Balasubramanian, Travis Jensen, Matteo Turilli, Peter M. Kasson, Michael R. Shirts, Shantenu Jha
2020 J jnl
The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations.
J. Comput. Aided Mol. Des.
Andrea Rizzi, Travis Jensen, David R. Slochower, Matteo Aldeghi, Vytautas Gapsys, Dimitris Ntekoumes, Stefano Bosisio, Michail Papadourakis, Niel M. Henriksen, Bert L. de Groot, Zoe Cournia, Alex Dickson, Julien Michel, Michael K. Gilson, Michael R. Shirts, David L. Mobley, John D. Chodera
2018 J jnl
Implementing Adaptive Ensemble Biomolecular Applications at Scale.
CoRR
Vivek Balasubramanian, Travis Jensen, Matteo Turilli, Peter M. Kasson, Michael R. Shirts, Shantenu Jha
2017 J jnl
Erratum to: Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset.
J. Comput. Aided Mol. Des.
Michael R. Shirts, Christoph Klein, Jason M. Swails, Jian Yin, Michael K. Gilson, David L. Mobley, David A. Case, Ellen D. Zhong
2017 J jnl
Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset.
J. Comput. Aided Mol. Des.
Michael R. Shirts, Christoph Klein, Jason M. Swails, Jian Yin, Michael K. Gilson, David L. Mobley, David A. Case, Ellen D. Zhong
2017 J jnl
Overview adcm43.bhtof the SAMPL5 host-guest challenge: Are we doing better?
J. Comput. Aided Mol. Des.
Jian Yin, Niel M. Henriksen, David R. Slochower, Michael R. Shirts, Michael Chiu, David L. Mobley, Michael K. Gilson
2016 J jnl
Blind prediction of cyclohexane-water distribution coefficients from the SAMPL5 challenge.
J. Comput. Aided Mol. Des.
Caitlin C. Bannan, Kalistyn H. Burley, Michael Chiu, Michael R. Shirts, Michael K. Gilson, David L. Mobley
2015 J jnl
Guidelines for the analysis of free energy calculations.
J. Comput. Aided Mol. Des.
Pavel V. Klimovich, Michael R. Shirts, David L. Mobley
2014 J jnl
Converging free energies of binding in cucurbit[7]uril and octa-acid host-guest systems from SAMPL4 using expanded ensemble simulations.
J. Comput. Aided Mol. Des.
Jacob I. Monroe, Michael R. Shirts
2013 J jnl
GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit.
Bioinform.
Sander Pronk, Szilárd Páll, Roland Schulz, Per Larsson, Pär Bjelkmar, Rossen Apostolov, Michael R. Shirts, Jeremy C. Smith, Peter M. Kasson, David van der Spoel, Berk Hess, Erik Lindahl
2013 J jnl
Identifying ligand binding sites and poses using GPU-accelerated Hamiltonian replica exchange molecular dynamics.
J. Comput. Aided Mol. Des.
Kai Wang, John D. Chodera, Yanzhi Yang, Michael R. Shirts