Oliver Beckstein

Orcid: 0000-0003-1340-0831

According to our database1, Oliver Beckstein authored at least 27 papers between 2011 and 2025.

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Bibliography

2025


2024



alchemlyb: the simple alchemistry library.
J. Open Source Softw., 2024

2023
MDAKits: A Framework for FAIR-Compliant Molecular Simulation Analysis.
Proceedings of the 22nd Python in Science Conference, 2023

2021
Precise force-field-based calculations of octanol-water partition coefficients for the SAMPL7 molecules.
J. Comput. Aided Mol. Des., 2021

MPI-parallel Molecular Dynamics Trajectory Analysis with the H5MD Format in the MDAnalysis Python Package.
Proceedings of the 20th Python in Science Conference, 2021

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.
J. Comput. Aided Mol. Des., 2020

Parallel performance of molecular dynamics trajectory analysis.
Concurr. Comput. Pract. Exp., 2020

2019
Correction: Path Similarity Analysis: A Method for Quantifying Macromolecular Pathways.
PLoS Comput. Biol., 2019

PMDA - Parallel Molecular Dynamics Analysis.
Proceedings of the 18th Python in Science Conference, 2019

Learning Everywhere: Pervasive Machine Learning for Effective High-Performance Computation.
Proceedings of the IEEE International Parallel and Distributed Processing Symposium Workshops, 2019

2018
SAMPL6: calculation of macroscopic pK a values from ab initio quantum mechanical free energies.
J. Comput. Aided Mol. Des., 2018

Task-parallel Analysis of Molecular Dynamics Trajectories.
CoRR, 2018

Task-parallel Analysis of Molecular Dynamics Trajectories.
Proceedings of the 47th International Conference on Parallel Processing, 2018

2017
Ligandbook: an online repository for small and drug-like molecule force field parameters.
Bioinform., 2017

Parallel Analysis in MDAnalysis using the Dask Parallel Computing Library.
Proceedings of the 16th Python in Science Conference, 2017

2016
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., 2016

MDAnalysis: A Python Package for the Rapid Analysis of Molecular Dynamics Simulations.
Proceedings of the 15th Python in Science Conference, 2016

datreant: persistent, Pythonic trees for heterogeneous data.
Proceedings of the 15th Python in Science Conference, 2016

2015
Path Similarity Analysis: A Method for Quantifying Macromolecular Pathways.
PLoS Comput. Biol., 2015

2014
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., 2014

2012
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., 2012

2011
Computing ensembles of transitions from stable states: Dynamic importance sampling.
J. Comput. Chem., 2011

MDAnalysis: A toolkit for the analysis of molecular dynamics simulations.
J. Comput. Chem., 2011


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