Oliver Beckstein

Publication Activity (10 Years)

Years Active: 2011-2021
Publications (10 Years): 18

Top Topics

Parallel Computing

Active Contour Model

Top Venues

J. Comput. Aided Mol. Des.

PLoS Comput. Biol.

Publications

Edis Jakupovic, Oliver Beckstein
MPI-parallel Molecular Dynamics Trajectory Analysis with the H5MD Format in the MDAnalysis Python Package. SciPy (2021)
Shujie Fan, Hristo Nedev, Ranjit Vijayan, Bogdan I. Iorga, Oliver Beckstein
Precise force-field-based calculations of octanol-water partition coefficients for the SAMPL7 molecules. J. Comput. Aided Mol. Des. 35 (7) (2021)
Shujie Fan, Bogdan I. Iorga, Oliver Beckstein
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. 34 (5) (2020)
Mahzad Khoshlessan, Ioannis Paraskevakos, Geoffrey C. Fox, Shantenu Jha, Oliver Beckstein
Parallel performance of molecular dynamics trajectory analysis. Concurr. Comput. Pract. Exp. 32 (19) (2020)
Sean L. Seyler, Avishek Kumar, M. F. Thorpe, Oliver Beckstein
Correction: Path Similarity Analysis: A Method for Quantifying Macromolecular Pathways. PLoS Comput. Biol. 15 (6) (2019)
Shujie Fan, Max Linke, Ioannis Paraskevakos, Richard J. Gowers, Michael Gecht, Oliver Beckstein
PMDA - Parallel Molecular Dynamics Analysis. SciPy (2019)
Mahzad Khoshlessan, Ioannis Paraskevakos, Geoffrey C. Fox, Shantenu Jha, Oliver Beckstein
Parallel Performance of Molecular Dynamics Trajectory Analysis. CoRR (2019)
Geoffrey C. Fox, James A. Glazier, J. C. S. Kadupitiya, Vikram Jadhao, Minje Kim, Judy Qiu, James P. Sluka, Endre T. Somogyi, Madhav Marathe, Abhijin Adiga, Jiangzhuo Chen, Oliver Beckstein, Shantenu Jha
Learning Everywhere: Pervasive Machine Learning for Effective High-Performance Computation. CoRR (2019)
Geoffrey C. Fox, James A. Glazier, J. C. S. Kadupitiya, Vikram Jadhao, Minje Kim, Judy Qiu, James P. Sluka, Endre T. Somogyi, Madhav Marathe, Abhijin Adiga, Jiangzhuo Chen, Oliver Beckstein, Shantenu Jha
Learning Everywhere: Pervasive Machine Learning for Effective High-Performance Computation. IPDPS Workshops (2019)
Ioannis Paraskevakos, André Luckow, Mahzad Khoshlessan, George Chantzialexiou, Thomas E. Cheatham, Oliver Beckstein, Geoffrey C. Fox, Shantenu Jha
Task-parallel Analysis of Molecular Dynamics Trajectories. ICPP (2018)
Edithe Selwa, Ian M. Kenney, Oliver Beckstein, Bogdan I. Iorga
SAMPL6: calculation of macroscopic pK a values from ab initio quantum mechanical free energies. J. Comput. Aided Mol. Des. 32 (10) (2018)
Ioannis Paraskevakos, André Luckow, George Chantzialexiou, Mahzad Khoshlessan, Oliver Beckstein, Geoffrey C. Fox, Shantenu Jha
Task-parallel Analysis of Molecular Dynamics Trajectories. CoRR (2018)
Jan J. Domanski, Oliver Beckstein, Bogdan I. Iorga
Ligandbook: an online repository for small and drug-like molecule force field parameters. Bioinform. 33 (11) (2017)
Mahzad Khoshlessan, Ioannis Paraskevakos, Shantenu Jha, Oliver Beckstein
Parallel Analysis in MDAnalysis using the Dask Parallel Computing Library. SciPy (2017)
David L. Dotson, Sean L. Seyler, Max Linke, Richard J. Gowers, Oliver Beckstein
datreant: persistent, Pythonic trees for heterogeneous data. SciPy (2016)
Ian M. Kenney, Oliver Beckstein, Bogdan I. Iorga
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. 30 (11) (2016)
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
MDAnalysis: A Python Package for the Rapid Analysis of Molecular Dynamics Simulations. SciPy (2016)
Sean L. Seyler, Avishek Kumar, M. F. Thorpe, Oliver Beckstein
Path Similarity Analysis: A Method for Quantifying Macromolecular Pathways. PLoS Comput. Biol. 11 (10) (2015)
Oliver Beckstein, Anaïs Fourrier, Bogdan I. Iorga
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. 28 (3) (2014)
Oliver Beckstein, Bogdan I. Iorga
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. 26 (5) (2012)
Juan R. Perilla, Oliver Beckstein, Elizabeth J. Denning, Thomas B. Woolf
Computing ensembles of transitions from stable states: Dynamic importance sampling. J. Comput. Chem. 32 (2) (2011)
Naveen Michaud-Agrawal, Elizabeth J. Denning, Thomas B. Woolf, Oliver Beckstein
MDAnalysis: A toolkit for the analysis of molecular dynamics simulations. J. Comput. Chem. 32 (10) (2011)