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Oliver Beckstein
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2020 – today
- 2024
- [j13]Zhiyi Wu
, David L. Dotson
alchemlyb: the simple alchemistry library. J. Open Source Softw. 9(101): 6934 (2024) - 2021
- [j12]Shujie Fan
Precise force-field-based calculations of octanol-water partition coefficients for the SAMPL7 molecules. J. Comput. Aided Mol. Des. 35(7): 853-870 (2021) - [c7]Edis Jakupovic, Oliver Beckstein:
MPI-parallel Molecular Dynamics Trajectory Analysis with the H5MD Format in the MDAnalysis Python Package. SciPy 2021: 40-48 - 2020
- [j11]Mahzad Khoshlessan, Ioannis Paraskevakos, Geoffrey C. Fox, Shantenu Jha
Parallel performance of molecular dynamics trajectory analysis. Concurr. Comput. Pract. Exp. 32(19) (2020) - [j10]Shujie Fan
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): 543-560 (2020)
2010 – 2019
- 2019
- [j9]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) - [c6]Geoffrey C. Fox, James A. Glazier, J. C. S. Kadupitiya, Vikram Jadhao, Minje Kim, Judy Qiu, James P. Sluka
Learning Everywhere: Pervasive Machine Learning for Effective High-Performance Computation. IPDPS Workshops 2019: 422-429 - [c5]Shujie Fan
PMDA - Parallel Molecular Dynamics Analysis. SciPy 2019: 134- - [i3]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:
Learning Everywhere: Pervasive Machine Learning for Effective High-Performance Computation. CoRR abs/1902.10810 (2019) - [i2]Mahzad Khoshlessan, Ioannis Paraskevakos, Geoffrey C. Fox, Shantenu Jha, Oliver Beckstein:
Parallel Performance of Molecular Dynamics Trajectory Analysis. CoRR abs/1907.00097 (2019) - 2018
- [j8]Edithe Selwa, Ian M. Kenney, Oliver Beckstein
SAMPL6: calculation of macroscopic pK a values from ab initio quantum mechanical free energies. J. Comput. Aided Mol. Des. 32(10): 1203-1216 (2018) - [c4]Ioannis Paraskevakos, André Luckow
Task-parallel Analysis of Molecular Dynamics Trajectories. ICPP 2018: 49:1-49:10 - [i1]Ioannis Paraskevakos, André Luckow, George Chantzialexiou, Mahzad Khoshlessan, Oliver Beckstein, Geoffrey C. Fox, Shantenu Jha:
Task-parallel Analysis of Molecular Dynamics Trajectories. CoRR abs/1801.07630 (2018) - 2017
- [j7]Jan J. Domanski, Oliver Beckstein, Bogdan I. Iorga
Ligandbook: an online repository for small and drug-like molecule force field parameters. Bioinform. 33(11): 1747-1749 (2017) - [c3]Mahzad Khoshlessan, Ioannis Paraskevakos, Shantenu Jha, Oliver Beckstein:
Parallel Analysis in MDAnalysis using the Dask Parallel Computing Library. SciPy 2017: 64-72 - 2016
- [j6]Ian M. Kenney, Oliver Beckstein
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): 1045-1058 (2016) - [c2]David L. Dotson
datreant: persistent, Pythonic trees for heterogeneous data. SciPy 2016: 51-56 - [c1]Richard J. Gowers, Max Linke, Jonathan Barnoud
MDAnalysis: A Python Package for the Rapid Analysis of Molecular Dynamics Simulations. SciPy 2016: 98-105 - 2015
- [j5]Sean L. Seyler
Path Similarity Analysis: A Method for Quantifying Macromolecular Pathways. PLoS Comput. Biol. 11(10) (2015) - 2014
- [j4]Oliver Beckstein
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): 265-276 (2014) - 2012
- [j3]Oliver Beckstein
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): 635-645 (2012) - 2011
- [j2]Juan R. Perilla
Computing ensembles of transitions from stable states: Dynamic importance sampling. J. Comput. Chem. 32(2): 196-209 (2011) - [j1]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): 2319-2327 (2011)
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