Data

Tools

Indexes

Applications

Experiments

Open Source Science

fegrow

An Open-Source Molecular Builder and Free Energy Preparation Workflow

https://github.com/cole-group/fegrow

Science Score: 85.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 4 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: nature.com
  • ✓
    Committers with academic emails
    1 of 7 committers (14.3%) from academic institutions
  • ✓
    Institutional organization owner
    Organization cole-group has institutional domain (blogs.ncl.ac.uk)
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (11.2%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

An Open-Source Molecular Builder and Free Energy Preparation Workflow

Basic Info
Statistics
  • Stars: 128
  • Watchers: 3
  • Forks: 22
  • Open Issues: 21
  • Releases: 8
Created over 4 years ago · Last pushed 6 months ago
Metadata Files
Readme Changelog License Citation

README.md

FEgrow 2.0.0: Active Learning and acceleration

A new release of FEgrow that adds active learning together with acceleration powered by Dask (multi -cpu, -node, -cluster).

To get started with the new functionality, see the tutorials folder, which contains examples of i) basic interactive molecular design, ii) an introduction to the chemspace functionality, and iii) an example of active learning for inhibitor design.

These notebooks are based on the functionality described in:

Cree B, Bieniek M, Amin S, Kawamura A, Cole D. Active learning driven prioritisation of compounds from on-demand libraries targeting the SARS-CoV-2 main protease. ChemRxiv (2024).

Scripts used to create Figures 2-6 in the above paper can be accessed here.

FEgrow (1.*)

An interactive workflow for building user-defined congeneric series of ligands in protein binding pockets for input to free energy calculations.

CIAnaconda-Server Badge

Bieniek, Mateusz K., Ben Cree, Rachael Pirie, Joshua T. Horton, Natalie J. Tatum, and Daniel J. Cole. "An open-source molecular builder and free energy preparation workflow." Communications Chemistry 5, no. 1 (2022): 136.

https://doi.org/10.1038/s42004-022-00754-9

Further Information

Please see cole-group.github.io/fegrow for full installation instructions, documentation and acknowledgements.

Owner

  • Name: cole-group
  • Login: cole-group
  • Kind: organization

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Bieniek"
  given-names: "Mateusz K"
  orcid: "https://orcid.org/0000-0002-3065-5417"
- family-names: "Cree"
  given-names: "Ben"
  orcid: "https://orcid.org/0000-0002-8934-973X"
- family-names: "Pirie"
  given-names: "Rachael"
  orcid: "https://orcid.org/0000-0002-2449-3458"
- family-names: "Horton"
  given-names: "Joshua T"
  orcid: "https://orcid.org/0000-0001-8694-7200"
- family-names: "Tatum"
  given-names: "Natalie J"
  orcid: "https://orcid.org/0000-0003-3878-9265"
- family-names: "Cole"
  given-names: "Daniel J"
  orcid: "https://orcid.org/0000-0003-2933-0719"
title: "An open-source molecular builder and free energy preparation workflow"
version: 1.0.2
doi: 10.1038/s42004-022-00754-9
date-released: 2022-07-22
url: "https://github.com/cole-group/FEgrow"

GitHub Events

Total
  • Create event: 19
  • Issues event: 7
  • Watch event: 11
  • Delete event: 9
  • Member event: 1
  • Issue comment event: 18
  • Push event: 49
  • Pull request review event: 2
  • Pull request review comment event: 2
  • Pull request event: 32
  • Fork event: 4
Last Year
  • Create event: 19
  • Issues event: 7
  • Watch event: 11
  • Delete event: 9
  • Member event: 1
  • Issue comment event: 18
  • Push event: 49
  • Pull request review event: 2
  • Pull request review comment event: 2
  • Pull request event: 32
  • Fork event: 4

Committers

Last synced: almost 3 years ago

All Time
  • Total Commits: 416
  • Total Committers: 7
  • Avg Commits per committer: 59.429
  • Development Distribution Score (DDS): 0.481
Past Year
  • Commits: 256
  • Committers: 5
  • Avg Commits per committer: 51.2
  • Development Distribution Score (DDS): 0.539
Top Committers
Name Email Commits
bieniekmat b****t@g****m 216
Mateusz Bieniek b****z@u****m 158
BenCree b****e@g****m 20
Ben Cree 6****e@u****m 9
Josh Horton J****n@n****k 8
djcole56 3****6@u****m 4
Rachael Pirie 5****6@u****m 1
Committer Domains (Top 20 + Academic)
newcastle.ac.uk: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 24
  • Total pull requests: 46
  • Average time to close issues: 2 days
  • Average time to close pull requests: 8 days
  • Total issue authors: 11
  • Total pull request authors: 4
  • Average comments per issue: 2.04
  • Average comments per pull request: 0.24
  • Merged pull requests: 41
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 12
  • Pull requests: 26
  • Average time to close issues: about 13 hours
  • Average time to close pull requests: 15 days
  • Issue authors: 6
  • Pull request authors: 4
  • Average comments per issue: 2.0
  • Average comments per pull request: 0.31
  • Merged pull requests: 22
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • bieniekmateusz (10)
  • velocirraptor23 (3)
  • ven828 (2)
  • jeeberhardt (2)
  • annamherz (2)
  • Kunal4774 (1)
  • Dslab2025 (1)
  • dww100 (1)
  • richardjgowers (1)
  • RPirie96 (1)
  • juliaLopanskaia (1)
  • amin-sagar (1)
  • noahharrison64 (1)
  • fjclark (1)
Pull Request Authors
  • bieniekmateusz (43)
  • jthorton (8)
  • djcole56 (8)
  • BenCree (7)
  • RPirie96 (2)
  • Mengo-ye (1)
  • fjclark (1)
Top Labels
Issue Labels
enhancement (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads: unknown
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 1
conda-forge.org: fegrow

FEgrow is an interactive workflow for building user-defined congeneric series of ligands in protein binding pockets for input to free energy calculations. Furthermore, FEgrow was extended in 2.0.0 to support Active Learning and scaling with Dask.

  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent repos count: 34.0%
Stargazers count: 40.1%
Average: 41.9%
Forks count: 42.2%
Dependent packages count: 51.2%
Last synced: 6 months ago

Dependencies

.github/workflows/CI.yml actions
  • actions/checkout v3 composite
  • conda-incubator/setup-miniconda v2.1.1 composite
.github/workflows/pylint.yml actions
  • actions/checkout v3 composite
  • actions/setup-python v3 composite
pyproject.toml pypi