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Journal Articles
- 2024
[j15]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): 1290-1305 (2024)- [j14]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:
alchemlyb: the simple alchemistry library. J. Open Source Softw. 9(101): 6934 (2024) - 2022
- [j13]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): 313-328 (2022) - [j12]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): 874-889 (2022) - [j11]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): 3981 (2022) - 2020
- [j10]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): 601-633 (2020) - [j9]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): 104 (2020) - 2017
- [j8]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): 1-19 (2017) - [j7]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): 147-161 (2017) - [j6]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): 777 (2017) - 2016
- [j5]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): 927-944 (2016) - 2015
- [j4]Pavel V. Klimovich, Michael R. Shirts, David L. Mobley:
Guidelines for the analysis of free energy calculations. J. Comput. Aided Mol. Des. 29(5): 397-411 (2015) - 2014
- [j3]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): 401-415 (2014) - 2013
- [j2]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): 845-854 (2013) - [j1]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): 989-1007 (2013)
Informal and Other Publications
- 2018
- [i1]Vivek Balasubramanian, Travis Jensen, Matteo Turilli, Peter M. Kasson, Michael R. Shirts, Shantenu Jha:
Implementing Adaptive Ensemble Biomolecular Applications at Scale. CoRR abs/1804.04736 (2018)
Coauthor Index
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