Oliver Beckstein

24 papers B 1Journal 16Unranked 7
YearRankTypeTitle / Venue / Authors
2024 J jnl
alchemlyb: the simple alchemistry library.
J. Open Source Softw.
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
2023 — conf
MDAKits: A Framework for FAIR-Compliant Molecular Simulation Analysis.
SciPy
Irfan Alibay, Lily Wang, Fiona Naughton, Ian M. Kenney, Jonathan Barnoud, Richard J. Gowers, Oliver Beckstein
2021 — conf
MPI-parallel Molecular Dynamics Trajectory Analysis with the H5MD Format in the MDAnalysis Python Package.
SciPy
Edis Jakupovic, Oliver Beckstein
2021 J jnl
Precise force-field-based calculations of octanol-water partition coefficients for the SAMPL7 molecules.
J. Comput. Aided Mol. Des.
Shujie Fan, Hristo Nedev, Ranjit Vijayan, Bogdan I. Iorga, Oliver Beckstein
2020 J jnl
Parallel performance of molecular dynamics trajectory analysis.
Concurr. Comput. Pract. Exp.
Mahzad Khoshlessan, Ioannis Paraskevakos, Geoffrey C. Fox, Shantenu Jha, Oliver Beckstein
2020 J jnl
Prediction of octanol-water partition coefficients for the SAMPL6-log P molecules using molecular dynamics simulations with OPLS-AA, AMBER and CHARMM force fields.
J. Comput. Aided Mol. Des.
Shujie Fan, Bogdan I. Iorga, Oliver Beckstein
2019 J jnl
Correction: Path Similarity Analysis: A Method for Quantifying Macromolecular Pathways.
PLoS Comput. Biol.
Sean L. Seyler, Avishek Kumar, M. F. Thorpe, Oliver Beckstein
2019 — conf
Learning Everywhere: Pervasive Machine Learning for Effective High-Performance Computation.
IPDPS Workshops
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, Shantenu Jha
2019 J jnl
Learning Everywhere: Pervasive Machine Learning for Effective High-Performance Computation.
CoRR
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, Shantenu Jha
2019 — conf
PMDA - Parallel Molecular Dynamics Analysis.
SciPy
Shujie Fan, Max Linke, Ioannis Paraskevakos, Richard J. Gowers, Michael Gecht, Oliver Beckstein
2019 J jnl
Parallel Performance of Molecular Dynamics Trajectory Analysis.
CoRR
Mahzad Khoshlessan, Ioannis Paraskevakos, Geoffrey C. Fox, Shantenu Jha, Oliver Beckstein
2018 J jnl
SAMPL6: calculation of macroscopic pK a values from ab initio quantum mechanical free energies.
J. Comput. Aided Mol. Des.
Edithe Selwa, Ian M. Kenney, Oliver Beckstein, Bogdan I. Iorga
2018 B conf
Task-parallel Analysis of Molecular Dynamics Trajectories.
ICPP
Ioannis Paraskevakos, André Luckow, Mahzad Khoshlessan, George Chantzialexiou, Thomas E. Cheatham, Oliver Beckstein, Geoffrey C. Fox, Shantenu Jha
2018 J jnl
Task-parallel Analysis of Molecular Dynamics Trajectories.
CoRR
Ioannis Paraskevakos, André Luckow, George Chantzialexiou, Mahzad Khoshlessan, Oliver Beckstein, Geoffrey C. Fox, Shantenu Jha
2017 J jnl
Ligandbook: an online repository for small and drug-like molecule force field parameters.
Bioinform.
Jan J. Domanski, Oliver Beckstein, Bogdan I. Iorga
2017 — conf
Parallel Analysis in MDAnalysis using the Dask Parallel Computing Library.
SciPy
Mahzad Khoshlessan, Ioannis Paraskevakos, Shantenu Jha, Oliver Beckstein
2016 — conf
MDAnalysis: A Python Package for the Rapid Analysis of Molecular Dynamics Simulations.
SciPy
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
2016 J jnl
Prediction of cyclohexane-water distribution coefficients for the SAMPL5 data set using molecular dynamics simulations with the OPLS-AA force field.
J. Comput. Aided Mol. Des.
Ian M. Kenney, Oliver Beckstein, Bogdan I. Iorga
2016 — conf
datreant: persistent, Pythonic trees for heterogeneous data.
SciPy
David L. Dotson, Sean L. Seyler, Max Linke, Richard J. Gowers, Oliver Beckstein
2015 J jnl
Path Similarity Analysis: A Method for Quantifying Macromolecular Pathways.
PLoS Comput. Biol.
Sean L. Seyler, Avishek Kumar, M. F. Thorpe, Oliver Beckstein
2014 J jnl
Prediction of hydration free energies for the SAMPL4 diverse set of compounds using molecular dynamics simulations with the OPLS-AA force field.
J. Comput. Aided Mol. Des.
Oliver Beckstein, Anaïs Fourrier, Bogdan I. Iorga
2012 J jnl
Prediction of hydration free energies for aliphatic and aromatic chloro derivatives using molecular dynamics simulations with the OPLS-AA force field.
J. Comput. Aided Mol. Des.
Oliver Beckstein, Bogdan I. Iorga
2011 J jnl
Computing ensembles of transitions from stable states: Dynamic importance sampling.
J. Comput. Chem.
Juan R. Perilla, Oliver Beckstein, Elizabeth J. Denning, Thomas B. Woolf
2011 J jnl
MDAnalysis: A toolkit for the analysis of molecular dynamics simulations.
J. Comput. Chem.
Naveen Michaud-Agrawal, Elizabeth J. Denning, Thomas B. Woolf, Oliver Beckstein