https://github.com/ale94mleon/BindFlow
A snakemake-based workflow for FEP and MM(PB/GB)SA calculations with GROMACS
https://github.com/ale94mleon/BindFlow
abfe drug-design drug-discovery fep high-throughput mmpbsa
Last synced: about 1 month ago
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A snakemake-based workflow for FEP and MM(PB/GB)SA calculations with GROMACS
- Host: GitHub
- URL: https://github.com/ale94mleon/BindFlow
- Owner: ale94mleon
- License: gpl-3.0
- Created: 2023-05-09T19:58:58.000Z (about 3 years ago)
- Default Branch: main
- Last Pushed: 2026-05-09T22:57:07.000Z (about 1 month ago)
- Last Synced: 2026-05-10T00:40:47.889Z (about 1 month ago)
- Topics: abfe, drug-design, drug-discovery, fep, high-throughput, mmpbsa
- Language: Python
- Homepage: https://bindflow.readthedocs.io
- Size: 6.51 MB
- Stars: 153
- Watchers: 2
- Forks: 17
- Open Issues: 13
-
Metadata Files:
- Readme: README.rst
- License: LICENSE
Awesome Lists containing this project
README
BindFlow
========
|logo|
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* - **Documentation**
- |docs|
* - **Source Code**
- |github|
* - **Build**
- |pypi-version|
* - **Python Versions**
- |pyversions|
* - **Dependencies**
- |rdkit|
* - **License**
- |license|
Description
-----------
**BindFlow** is a snakemake-based workflow for ABFE calculations using GROMACS.
Documentation
-------------
The installation instructions, documentation and tutorials can be found online on `ReadTheDocs `_.
Issues
------
If you have found a bug, please open an issue on the `GitHub Issues `_.
Discussion
----------
If you have questions on how to use **BindFlow**, or if you want to give feedback or share ideas and new features, please head to the `GitHub Discussions `_.
Citing **BindFlow**
-------------------
Please refer to the `citation page `__ on the documentation.
Funding
-------
This project received funding from `Marie Skłodowska-Curie Actions `__. It was developed in the
`Computational Biophysics Group `__ of `Saarland University `__.
Acknowledgment
--------------
This project was forked from `ABFE_workflow `__.
.. |logo| image:: https://github.com/ale94mleon/BindFlow/blob/main/docs/source/_static/BindFlow-logo-full.svg?raw=true
:target: https://github.com/ale94mleon/BindFlow/
:alt: logo
.. |docs| image:: https://readthedocs.org/projects/BindFlow/badge/?version=latest
:target: https://BindFlow.readthedocs.io/en/latest/?badge=latest
:alt: Documentation
.. .. |binder| image:: https://mybinder.org/badge_logo.svg
.. :target: https://mybinder.org/v2/gh/ale94mleon/BindFlow/HEAD?labpath=%2Fdocs%2Fnotebooks%2F
.. :alt: binder
.. .. |tests| image:: https://github.com/ale94mleon/BindFlow/actions/workflows/tests.yml/badge.svg
.. :target: https://github.com/ale94mleon/BindFlow/actions/workflows/tests.yml
.. :alt: tests
.. .. |codacy-codecove| image:: https://app.codacy.com/project/badge/Coverage/08a3ac7c13df4339b8a1da0e8d31810e
.. :target: https://app.codacy.com/gh/ale94mleon/BindFlow/dashboard?utm_source=gh&utm_medium=referral&utm_content=&utm_campaign=Badge_coverage
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.. :alt: codacy-grade
.. .. |CodeQL| image:: https://github.com/ale94mleon/BindFlow/actions/workflows/codeql-analysis.yml/badge.svg
.. :target: https://github.com/ale94mleon/BindFlow/actions/workflows/codeql-analysis.yml
.. :alt: CodeQL
.. |pypi-version| image:: https://img.shields.io/pypi/v/bindflow.svg
:target: https://pypi.python.org/pypi/bindflow/
:alt: pypi-version
.. .. |conda| image:: https://anaconda.org/ale94mleon/BindFlow/badges/version.svg
.. :target: https://anaconda.org/ale94mleon/BindFlow
.. :alt: conda
.. |github| image:: https://badgen.net/badge/icon/github?icon=github&label
:target: https://github.com/ale94mleon/BindFlow
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:target: https://www.rdkit.org/docs/index.html
:alt: rdkit
.. .. |meeko| image:: https://img.shields.io/static/v1?label=Powered%20by&message=Meeko&color=6858ff&style=flat
.. :target: https://github.com/forlilab/Meeko
.. :alt: Meeko
.. .. |crem| image:: https://img.shields.io/static/v1?label=Powered%20by&message=CReM&color=9438ff&style=flat
.. :target: https://crem.readthedocs.io/en/latest/
.. :alt: crem
.. |license| image:: https://img.shields.io/badge/License-GPLv3-green
:target: https://github.com/ale94mleon/bindflow/
:alt: license
.. .. |downloads| image:: https://static.pepy.tech/personalized-badge/bindflow?period=total&units=international_system&left_color=grey&right_color=brightgreen&left_text=Downloads
.. :target: https://pepy.tech/project/bindflow
.. :alt: download