Michael R. Shirts

Publication Activity (10 Years)

Years Active: 2013-2024
Publications (10 Years): 11

Top Topics

Lessons Learned

Molecular Dynamics

Top Venues

J. Comput. Aided Mol. Des.

J. Chem. Inf. Model.

SN Comput. Sci.

Publications

Connor M. Davel, Timotej Bernat, Jeffrey R. Wagner, Michael R. Shirts
Parameterization of General Organic Polymers within the Open Force Field Framework. J. Chem. Inf. Model. 64 (4) (2024)
Wei-Tse Hsu, Dominique A. Ramirez, Tarek Sammakia, Zhongping Tan, Michael R. Shirts
Identifying signatures of proteolytic stability and monomeric propensity in O-glycosylated insulin using molecular simulation. J. Comput. Aided Mol. Des. 36 (4) (2022)
Owen Madin, Simon Boothroyd, Richard A. Messerly, Josh Fass, John D. Chodera, Michael R. Shirts
Bayesian-Inference-Driven Model Parametrization and Model Selection for 2CLJQ Fluid Models. J. Chem. Inf. Model. 62 (4) (2022)
Pascal T. Merz, Wei-Tse Hsu, Matt W. Thompson, Simon Boothroyd, Chris C. Walker, Michael R. Shirts
physical_validation: A Python package to assess the physical validity of molecular simulation results. J. Open Source Softw. 7 (69) (2022)
Vivek Balasubramanian, Travis Jensen, Matteo Turilli, Peter M. Kasson, Michael R. Shirts, Shantenu Jha
Adaptive Ensemble Biomolecular Applications at Scale. SN Comput. Sci. 1 (2) (2020)
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
The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations. J. Comput. Aided Mol. Des. 34 (5) (2020)
Vivek Balasubramanian, Travis Jensen, Matteo Turilli, Peter M. Kasson, Michael R. Shirts, Shantenu Jha
Implementing Adaptive Ensemble Biomolecular Applications at Scale. CoRR (2018)
Michael R. Shirts, Christoph Klein, Jason M. Swails, Jian Yin, Michael K. Gilson, David L. Mobley, David A. Case, Ellen D. Zhong
Erratum to: Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset. J. Comput. Aided Mol. Des. 31 (8) (2017)
Jian Yin, Niel M. Henriksen, David R. Slochower, Michael R. Shirts, Michael Chiu, David L. Mobley, Michael K. Gilson
Overview adcm43.bhtof the SAMPL5 host-guest challenge: Are we doing better? J. Comput. Aided Mol. Des. 31 (1) (2017)
Michael R. Shirts, Christoph Klein, Jason M. Swails, Jian Yin, Michael K. Gilson, David L. Mobley, David A. Case, Ellen D. Zhong
Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset. J. Comput. Aided Mol. Des. 31 (1) (2017)
Caitlin C. Bannan, Kalistyn H. Burley, Michael Chiu, Michael R. Shirts, Michael K. Gilson, David L. Mobley
Blind prediction of cyclohexane-water distribution coefficients from the SAMPL5 challenge. J. Comput. Aided Mol. Des. 30 (11) (2016)
Pavel V. Klimovich, Michael R. Shirts, David L. Mobley
Guidelines for the analysis of free energy calculations. J. Comput. Aided Mol. Des. 29 (5) (2015)
Jacob I. Monroe, Michael R. Shirts
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. 28 (4) (2014)
Kai Wang, John D. Chodera, Yanzhi Yang, Michael R. Shirts
Identifying ligand binding sites and poses using GPU-accelerated Hamiltonian replica exchange molecular dynamics. J. Comput. Aided Mol. Des. 27 (12) (2013)
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
GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit. Bioinform. 29 (7) (2013)