Michael R. Shirts

According to our database, Michael R. Shirts authored at least 15 papers between 2013 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2024

Parameterization of General Organic Polymers within the Open Force Field Framework.

Connor M. Davel, Timotej Bernat, Jeffrey R. Wagner, Michael R. Shirts

J. Chem. Inf. Model., February, 2024

2022

physical_validation: A Python package to assess the physical validity of molecular simulation results.

Pascal T. Merz, Wei-Tse Hsu, Matt W. Thompson, Simon Boothroyd, Chris C. Walker, Michael R. Shirts

J. Open Source Softw., 2022

Bayesian-Inference-Driven Model Parametrization and Model Selection for 2CLJQ Fluid Models.

Owen Madin, Simon Boothroyd, Richard A. Messerly, Josh Fass, John D. Chodera, Michael R. Shirts

J. Chem. Inf. Model., 2022

Identifying signatures of proteolytic stability and monomeric propensity in O-glycosylated insulin using molecular simulation.

Wei-Tse Hsu, Dominique A. Ramirez, Tarek Sammakia, Zhongping Tan, Michael R. Shirts

J. Comput. Aided Mol. Des., 2022

2020

Adaptive Ensemble Biomolecular Applications at Scale.

Vivek Balasubramanian, Travis Jensen, Matteo Turilli, Peter M. Kasson, Michael R. Shirts, Shantenu Jha

SN Comput. Sci., 2020

The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations.

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

J. Comput. Aided Mol. Des., 2020

2018

Implementing Adaptive Ensemble Biomolecular Applications at Scale.

Vivek Balasubramanian, Travis Jensen, Matteo Turilli, Peter M. Kasson, Michael R. Shirts, Shantenu Jha

CoRR, 2018

2017

Overview adcm43.bhtof the SAMPL5 host-guest challenge: Are we doing better?

Jian Yin, Niel M. Henriksen, David R. Slochower, Michael R. Shirts, Michael Chiu, David L. Mobley, Michael K. Gilson

J. Comput. Aided Mol. Des., 2017

Erratum to: Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset.

Michael R. Shirts, Christoph Klein, Jason M. Swails, Jian Yin, Michael K. Gilson, David L. Mobley, David A. Case, Ellen D. Zhong

J. Comput. Aided Mol. Des., 2017

Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset.

Michael R. Shirts, Christoph Klein, Jason M. Swails, Jian Yin, Michael K. Gilson, David L. Mobley, David A. Case, Ellen D. Zhong

J. Comput. Aided Mol. Des., 2017

2016

Blind prediction of cyclohexane-water distribution coefficients from the SAMPL5 challenge.

Caitlin C. Bannan, Kalistyn H. Burley, Michael Chiu, Michael R. Shirts, Michael K. Gilson, David L. Mobley

J. Comput. Aided Mol. Des., 2016

2015

Guidelines for the analysis of free energy calculations.

Pavel V. Klimovich, Michael R. Shirts, David L. Mobley

J. Comput. Aided Mol. Des., 2015

2014

Converging free energies of binding in cucurbit[7]uril and octa-acid host-guest systems from SAMPL4 using expanded ensemble simulations.

Jacob I. Monroe, Michael R. Shirts

J. Comput. Aided Mol. Des., 2014

2013

Identifying ligand binding sites and poses using GPU-accelerated Hamiltonian replica exchange molecular dynamics.

Kai Wang, John D. Chodera, Yanzhi Yang, Michael R. Shirts

J. Comput. Aided Mol. Des., 2013

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit.

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

Bioinform., 2013