Author

John D Chodera

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Biochemistry· 1 Bioinformatics· 1 Biophysics· 1

Signature Assays, Organisms & Methods

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Approach:statistical model· 3 Research Focus:benchmarking· 2 Approach:deep learning· 2 Assay:multiome· 1 Assay:protein structure· 1 Research Focus:software / tool· 1

Frequent Co-Authors

Sonya M Hanson· 2 shared Daniel L Parton· 1 shared Kyle A Beauchamp· 1 shared Patrick B Grinaway· 1 shared Sean Ekins· 1 shared

Activity by Year

2015-2016 · peak 2/yr

Co-Author Collaboration Network

5 top collaborators · 7 mutual co-author links

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2 shared papersBioinformatics

Sonya M Hanson

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3 papers

Recent·Most cited

Ensembler: Enabling high-throughput molecular simulations at the superfamily scale

Daniel L Parton, Patrick B Grinaway, Sonya M Hanson, Kyle A Beauchamp, John D Chodera

Ensembler automates the preparation of protein structures for high-throughput molecular simulations across entire superfamilies.

PLOS Computational Biology · Jun 23, 2016Peer-reviewedBioinformatics

A simple method for automated equilibration detection in molecular simulations

The paper introduces an automated method to detect equilibration in molecular simulations by maximizing uncorrelated samples, and provides a Python implementation.

bioRxiv · Dec 30, 2015Biophysics

Modeling error in experimental assays using the bootstrap principle: Understanding discrepancies between assays using different dispensing technologies

Sonya M Hanson, Sean Ekins, John D Chodera

The paper models error in experimental assays using the bootstrap principle to understand and correct discrepancies caused by different dispensing technologies.

bioRxiv · Dec 9, 2015Biochemistry