MDAnalysis: A toolkit for the analysis of molecular dynamics simulations. - Naveen Michaud-Agrawal; Elizabeth J. Denning; Thomas B. Woolf; Oliver Beckstein (J. Comput. Chem., 2011)

Computing ensembles of transitions from stable states: Dynamic importance sampling. - Juan R. Perilla; Oliver Beckstein; Elizabeth J. Denning; Thomas B. Woolf (J. Comput. Chem., 2011)

Prediction of hydration free energies for aliphatic and aromatic chloro derivatives using molecular dynamics simulations with the OPLS-AA force field. - Oliver Beckstein; Bogdan I. Iorga (J. Comput. Aided Mol. Des., 2012)

Prediction of hydration free energies for the SAMPL4 diverse set of compounds using molecular dynamics simulations with the OPLS-AA force field. - Oliver Beckstein; Anaïs Fourrier; Bogdan I. Iorga (J. Comput. Aided Mol. Des., 2014)

Path Similarity Analysis: A Method for Quantifying Macromolecular Pathways. - Sean L. Seyler; Avishek Kumar; M. F. Thorpe; Oliver Beckstein (PLoS Comput. Biol., 2015)

datreant: persistent, Pythonic trees for heterogeneous data. - David L. Dotson; Sean L. Seyler; Max Linke; Richard J. Gowers; Oliver Beckstein (SciPy, 2016)

MDAnalysis: A Python Package for the Rapid Analysis of Molecular Dynamics Simulations. - Richard J. Gowers; Max Linke; Jonathan Barnoud; Tyler J. E. Reddy; Manuel N. Melo; Sean L. Seyler; Jan J. Domanski; David L. Dotson; Sébastien Buchoux; Ian M. Kenney; Oliver Beckstein (SciPy, 2016)

Prediction of cyclohexane-water distribution coefficients for the SAMPL5 data set using molecular dynamics simulations with the OPLS-AA force field. - Ian M. Kenney; Oliver Beckstein; Bogdan I. Iorga (J. Comput. Aided Mol. Des., 2016)

Parallel Analysis in MDAnalysis using the Dask Parallel Computing Library. - Mahzad Khoshlessan; Ioannis Paraskevakos; Shantenu Jha; Oliver Beckstein (SciPy, 2017)

Ligandbook: an online repository for small and drug-like molecule force field parameters. - Jan J. Domanski; Oliver Beckstein; Bogdan I. Iorga (Bioinform., 2017)

Task-parallel Analysis of Molecular Dynamics Trajectories. - Ioannis Paraskevakos; André Luckow; Mahzad Khoshlessan; George Chantzialexiou; Thomas E. Cheatham; Oliver Beckstein; Geoffrey C. Fox; Shantenu Jha (ICPP, 2018)

Task-parallel Analysis of Molecular Dynamics Trajectories. - Ioannis Paraskevakos; André Luckow; George Chantzialexiou; Mahzad Khoshlessan; Oliver Beckstein; Geoffrey C. Fox; Shantenu Jha (CoRR, 2018)

SAMPL6: calculation of macroscopic pK a values from ab initio quantum mechanical free energies. - Edithe Selwa; Ian M. Kenney; Oliver Beckstein; Bogdan I. Iorga (J. Comput. Aided Mol. Des., 2018)

Learning Everywhere: Pervasive Machine Learning for Effective High-Performance Computation. - Geoffrey C. Fox; James A. Glazier; J. C. S. Kadupitiya; Vikram Jadhao; Minje Kim; Judy Qiu; James P. Sluka; Endre T. Somogyi; Madhav V. Marathe; Abhijin Adiga; Jiangzhuo Chen; Oliver Beckstein; et al. (IPDPS Workshops, 2019)

PMDA - Parallel Molecular Dynamics Analysis. - Shujie Fan; Max Linke; Ioannis Paraskevakos; Richard J. Gowers; Michael Gecht; Oliver Beckstein (SciPy, 2019)

Correction: Path Similarity Analysis: A Method for Quantifying Macromolecular Pathways. - Sean L. Seyler; Avishek Kumar; M. F. Thorpe; Oliver Beckstein (PLoS Comput. Biol., 2019)

Parallel performance of molecular dynamics trajectory analysis. - Mahzad Khoshlessan; Ioannis Paraskevakos; Geoffrey C. Fox; Shantenu Jha; Oliver Beckstein (Concurr. Comput. Pract. Exp., 2020)

Prediction of octanol-water partition coefficients for the SAMPL6-log P molecules using molecular dynamics simulations with OPLS-AA, AMBER and CHARMM force fields. - Shujie Fan; Bogdan I. Iorga; Oliver Beckstein (J. Comput. Aided Mol. Des., 2020)

MPI-parallel Molecular Dynamics Trajectory Analysis with the H5MD Format in the MDAnalysis Python Package. - Edis Jakupovic; Oliver Beckstein (SciPy, 2021)

Precise force-field-based calculations of octanol-water partition coefficients for the SAMPL7 molecules. - Shujie Fan; Hristo Nedev; Ranjit Vijayan; Bogdan I. Iorga; Oliver Beckstein (J. Comput. Aided Mol. Des., 2021)

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)

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)