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MobleyLab / benchmarksets

Benchmark sets for binding free energy calculations: Perpetual review paper, discussion, datasets, and standards
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Benchmark sets for free energy calculations

This repository relates to the perpetual review (definition) paper called "Predicting binding free energies: Frontiers and benchmarks" by David L. Mobley, Germano Heinzelmann, Niel M. Henriksen, and Michael K. Gilson. The repository's focus is benchmark sets for binding free energy calculations, including the perpetual review paper, but also supporting files and other materials relating to free energy benchmarks. Thus, the repository includes not only the perpetual review paper but also further discussion, datasets, and (hopefully ultimately) standards for datasets and data deposition.

The latest version of the paper is always available on this GitHub repository, as well as all previous versions. Additionally, all release versions -- current and prior -- are available via Zenodo DOIs, with the latest release at this DOI: DOI

The paper

Versions

The most up-to-date version of our perpetual review paper always available here. Additionally, this repository provides the authoritative source for all versions of this paper. Released versions of the paper are also archived as preprints on eScholarship, and have Zenodo DOIs as noted above. An early version of this work was published in Annual Review of Biophysics 46:531-558 (2017).

Publication in Annual Review

While a portion of this work was originally published with Annual Review, the version here is substantially expanded and updated, and will continue to deviate further from the AR version. Thus, we refer to this version as the "perpetual review version" and this is refelected in its title.

Ongoing updates and credit

Source files for the paper are deposited here on this GitHub repository, as detailed below, and comments/suggestions, etc. are welcome via the issue tracker (https://github.com/MobleyLab/benchmarksets/issues).

The Annual Review portion of this work is posted with permission from the Annual Review of Biophysics, Volume 46 © 2017 by Annual Reviews. Only the Annual Reviews version of the work is peer reviewed; versions posted here are effectively preprints updated at the authors' discretion. The right to create derivative works (exercised here) is also exercised with permission from the Annual Review of Biophysics, Volume 46 © 2017 by Annual Reviews, http://www.annualreviews.org/

A list of authors is provided below.

Citing this work

To cite this work, please cite both:

The vision

The field vitally needs benchmark sets to test and advance free energy calculations, as we detail in our paper. Currently, there are no such standard benchmark systems. And when good test systems are found, the relevant data tends to be published but then forgotten, and never becomes widely available. Here, we want the community to be involved in selecting benchmark systems, highlighting their key challenges, and making the data and results readily available to drive new science.

To make this happen, we need community input. Please bring new, relevant work to our attention, including experimental or modeling work on the benchmark systems currently available here, or new work on systems that might make good candidate benchmark systems for the future. And please help us create consensus around a modest set of benchmark systems which can be used to drive forward progress in the field.

The benchmark sets

Currently proposed benchmark sets are detailed in the paper and include:

Other near-term candidates include:

Community involvement is needed to pick and advance the best benchmarks.

Get involved

We need your help to pick the most informative systems, identify the challenges they present, and help make them standard benchmarks. Please provide your input:

Vote on what we should do next

For long-term directions, please help us prioritize what we ought to be doing in terms of benchmarks and other changes. Please click below to vote on one of these priorities or to suggest your own (such as addition of specific benchmark systems):

Feature Requests

Submit an issue

If you have a specific suggestion or request relating to the material on GitHub or our paper, please submit a request on our issue tracker.

Submit a pull request

We also welcome contributions to the material which is already here to extend it (see Section IV in our paper) and encourage you to actually propose changes via a "pull request", even to the paper itself. This will allow us to track your contributions, as well. Specifically, the full list of contributors to the updated paper and data can be appended to subsequent versions of this work, as they would be for a software project. New versions of this work are assigned unique, cite-able DOIs and essentially constitute preprints, so they can be cited as interim research products.

Authors

Your name, too, can go here if you help us substantially revise/extend the paper.

Acknowledgments

We want to thank the following people who contributed to this repository and the paper, in addition to those acknowledged within the text itself

Please note that GitHub's automatic "contributors" list does not provide a full accounting of everyone contributing to this work, as some contributions have been received by e-mail or other mechanisms.

Versions

Changes not yet in a release

Manifest