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)

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)

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)

Guidelines for the analysis of free energy calculations. - Pavel V. Klimovich; Michael R. Shirts; David L. Mobley (J. Comput. Aided Mol. Des., 2015)

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)

Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset. - Michael R. Shirts; Christoph Klein 003; Jason M. Swails; Jian Yin 005; Michael K. Gilson; David L. Mobley; David A. Case; Ellen D. Zhong (J. Comput. Aided Mol. Des., 2017)

Erratum to: Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset. - Michael R. Shirts; Christoph Klein 003; Jason M. Swails; Jian Yin 005; Michael K. Gilson; David L. Mobley; David A. Case; Ellen D. Zhong (J. Comput. Aided Mol. Des., 2017)

Overview adcm43.bhtof the SAMPL5 host-guest challenge: Are we doing better? - Jian Yin 005; Niel M. Henriksen; David R. Slochower; Michael R. Shirts; Michael Chiu; David L. Mobley; Michael K. Gilson (J. Comput. Aided Mol. Des., 2017)

Implementing Adaptive Ensemble Biomolecular Applications at Scale. - Vivek Balasubramanian; Travis Jensen; Matteo Turilli; Peter M. Kasson; Michael R. Shirts; Shantenu Jha (CoRR, 2018)

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; et al. (J. Comput. Aided Mol. Des., 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)

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)

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)

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)

alchemlyb: the simple alchemistry library. - 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; et al. (J. Open Source Softw., 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., 2024)

alchemlyb. - David L. Dotson; Ian M. Kenney; Oliver Beckstein; Shuai Liu; Travis Jensen; Bryce K. Allen; Dominik Wille; Victoria T. Lim; Hyungro Lee; Mohammad Soroush Barhaghi; Zhiyi Wu; Wei-Tse Hsu; et al. (Zenodo, 2024)

alchemlyb: the simple alchemistry library. - David L. Dotson; Ian M. Kenney; Oliver Beckstein; Shuai Liu; Travis Jensen; Bryce K. Allen; Dominik Wille; Victoria T. Lim; Hyungro Lee; Mohammad Soroush Barhaghi; Zhiyi Wu; Wei-Tse Hsu; et al. (Zenodo, 2024)

alchemlyb: the simple alchemistry library. - David L. Dotson; Ian M. Kenney; Oliver Beckstein; Shuai Liu; Travis Jensen; Bryce K. Allen; Dominik Wille; Victoria T. Lim; Hyungro Lee; Mohammad Soroush Barhaghi; Zhiyi Wu; Wei-Tse Hsu; et al. (Zenodo, 2024)