https://github.com/alchemistry/alchemical-best-practices
Best practice document for alchemical free energy calculations going to livecoms journal
Science Score: 26.0%
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Low similarity (13.2%) to scientific vocabulary
Repository
Best practice document for alchemical free energy calculations going to livecoms journal
Basic Info
- Host: GitHub
- Owner: alchemistry
- License: cc-by-4.0
- Language: Jupyter Notebook
- Default Branch: main
- Size: 239 MB
Statistics
- Stars: 76
- Watchers: 13
- Forks: 24
- Open Issues: 25
- Releases: 0
Metadata Files
README.md
Best Practices for Alchemical Free Energy Simulations
v2.0 Update
The original best practices guide will be split into two documents: the first will gives best practices for running a single calculation (and give details on theory/ system-specific setup), while the second will give best practices for running multiple calculations (with a focus on automation). The first (this manuscript) will become version 2.0 of the current guide, while the second will be submitted as a new manuscript (see this repo).
Goals
- Checklist and background for new practitioners of relative and absolute alchemical free energy calculations: What should you pay attention to in setting up and running calculations in common codes and why.
- Provide guidance to authors as to what should be reported about their protocols in a Methods section, either conforming to standard or reporting where they did not conform and why. Useful to reviewers as well.
Scope
Preparation (focused on aspects unique to alchemical free energies), execution, and analysis of:
- Transfer free energies (hydration free energies, partition coefficients, etc.)
- Binding free energies
List of Authors
(As ordered on the paper)
- Antonia S. J. S. Mey
- Bryce Allen
- Hannah E. Bruce Macdonald
- John D. Chodera
- David F. Hahn
- Maximilian Kuhn
- Julien Michel
- David L. Mobley
- Levi N. Naden
- Samarjeet Prasad
- Andrea Rizzi
- Jenke Scheen
- Michael R. Shirts
- Gary Tresadern
- Huafeng Xu
List of Contributors
(non-author list of people who contributed to document) - Julia Rice -- Attended initial discussion meeting at NIST in Aug. 2017
Paper Writing as Code Development
This paper is being developed as a living document, open to changes from the community. You can read more about the concept of writing a paper in the same way one would write software code in the essay "Paper writing as code development". If you have comments or suggestions, we welcome them! Please submit them as issues to this GitHub repository so they can be recorded and given credit for the contribution. Specific changes can be proposed via pull requests.
Online Resources
Original brainstorming document: (https://docs.google.com/document/d/1h7GIyOJykBWz-GPKtYZK-Pv7cbLbX8XTM2xLUpSppoE)
List of Released Versions
revisions for v 1.0
Owner
- Name: alchemistry.org
- Login: alchemistry
- Kind: organization
- Website: http://alchemistry.org
- Repositories: 8
- Profile: https://github.com/alchemistry
Advancing alchemical free energy calculations for small molecule design
GitHub Events
Total
- Create event: 5
- Issues event: 41
- Watch event: 14
- Delete event: 2
- Member event: 1
- Issue comment event: 213
- Push event: 22
- Pull request review comment event: 10
- Pull request review event: 14
- Pull request event: 17
- Fork event: 5
Last Year
- Create event: 5
- Issues event: 41
- Watch event: 14
- Delete event: 2
- Member event: 1
- Issue comment event: 213
- Push event: 22
- Pull request review comment event: 10
- Pull request review event: 14
- Pull request event: 17
- Fork event: 5
Issues and Pull Requests
Last synced: 10 months ago
All Time
- Total issues: 15
- Total pull requests: 11
- Average time to close issues: about 1 year
- Average time to close pull requests: over 1 year
- Total issue authors: 4
- Total pull request authors: 9
- Average comments per issue: 4.6
- Average comments per pull request: 0.91
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 12
- Pull requests: 9
- Average time to close issues: 6 months
- Average time to close pull requests: about 2 months
- Issue authors: 2
- Pull request authors: 8
- Average comments per issue: 3.83
- Average comments per pull request: 0.56
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- fjclark (18)
- sboresch (1)
- mrshirts (1)
- samarjeet (1)
- jchodera (1)
Pull Request Authors
- fjclark (4)
- samarjeet (1)
- sboresch (1)
- slochower (1)
- WillGPoole (1)
- hannahbruce (1)
- RiesBen (1)
- mrshirts (1)
- egallicc (1)