Science Score: 36.0%
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Low similarity (12.0%) to scientific vocabulary
Repository
binding free energy estimator 2
Basic Info
- Host: GitHub
- Owner: fhh2626
- License: gpl-3.0
- Language: Python
- Default Branch: main
- Size: 1.31 MB
Statistics
- Stars: 126
- Watchers: 7
- Forks: 39
- Open Issues: 27
- Releases: 22
Metadata Files
README.md
Binding Free Energy Estimator 3
Binding free energy estimator 3 (BFEE3) has come! There are three major upgrades in BFEE3: (1) LDDM, a high-throughput alchemical route for absolute binding free-energy calculations; (2) streamlined geometrical route for protein-protien binding free-energy calculations and (3) quick settings for common calculations.
BFEE is a python-based software that automates absolute binding free energy calculations through either the alchemical or geometric route by molecular dynamics simulations.
Theoretical backgrounds
The degrees of freedom of the protein-ligand (or host-guest) system are described by a series of geometric variables (or collective variables), as firstly described by the Karplus group. In BFEE, a generalized, best-fit-rotation-based geometric variables are used, making it in principle available to any protein-ligand complex. See this paper for introduction of these variables.
In the geometric route, the degrees of freedom is investigated one by one, through one-dimensional free-energy calculations. In BFEE, WTM-eABF is used, while other importance-sampling algorithms such as plain eABF are also acceptable.
The alchemical route is a variants of the double decoupling method (DDM). A thermodynamic cycle, in which the ligand and the geometric restraints are decoupled independently to guarantee the convergence of the simulations.
这里是标准结合自由能计算方法的中文介绍.
Features
Generates all the input files for absolute binding free energy calculations;
Support Protein-protein and protein-ligand complexes;
Perform post-treatment automatedly;
Support NAMD (alchemical and geometric route) and Gromacs (geometric route) as molecular dynamics engines;
Support many file formats for the input complex structure (PSF/PDB/PRM, PRM7/RST7, TOP/PDB);
Support both rigid (exclude RMSD CV) and flexible (include RMSD CV) ligands and protein-protein complexes (streamlined geometrical route);
...
Requirements
Python 3.6+, PySide 2, numpy, scipy, matplotlib, parmed and MDAnalysis.
NAMD 3.0 or later / GROMACS 2024 or later.
Note: Since both NAMD and Gromacs have incorporated Colvars in their latest binaries. Each release of BFEE3 corresponds to a version of NAMD/Gromacs. Please always use
the corresponding or later versions of the MD engines for free-energy calculations!
Installation
We suggest to install BFEE through conda. It will be safe if conda is install in a new environment
conda create --name bfee (optional)
conda activate bfee (optional)
conda install -c conda-forge BFEE2
Usage
Simply run BFEE2Gui.py in terminal or PowerShell. One may need to use the absolute path on MS Windows.
A step-by-step tutorial is provided here.
A tutorial about new streamlined geometrical route is provided in the SI of this paper.
Test files
One can download the Supplement Data here for testing BFEE3.
Citations
When possible, please consider mentioning Fu et al. Nat. Protoc. 2022, doi:10.1038/s41596-021-00676-1 when BFEE is used in your project.
Additional references:
BFEE2: Fu et al. J. Chem. Inf. Model. 2021, 61, 2116–2123
BFEE2 for protein-protein binding free energy calculations Fu et al. J. Chem. Inf. Model. 2023, 63, 2512–2519
Alchemical and geometric routes Gumbart et al. J. Chem. Theory Comput. 2013, 9, 794–802
WTM-eABF: Fu et al. Acc. Chem. Res. 2019, 52, 3254–3264 and Fu et al. J. Phys. Chem. Lett. 2018, 9, 4738–4745
Collective variables: Fu et al. J. Chem. Theory Comput. 2017, 13, 5173–5178
Colvars module: Fiorin et al. Mol. Phys. 2013 111, 3345-3362
"Mother" of all restraint-based binding free-energy calculations: Hermans et al. Isr. J. Chem. 1986, 27, 225–227
Contact us
This software is under the GPLv3 license. For more information about BFEE, contact Haohao Fu (fhh2626@nankai.edu.cn) and Haochuan Chen (yjcoshc@mail.nankai.edu.cn).
Owner
- Login: fhh2626
- Kind: user
- Repositories: 6
- Profile: https://github.com/fhh2626
GitHub Events
Total
- Issues event: 8
- Watch event: 18
- Issue comment event: 30
- Push event: 12
- Pull request review comment event: 2
- Pull request review event: 3
- Pull request event: 9
- Fork event: 4
Last Year
- Issues event: 8
- Watch event: 18
- Issue comment event: 30
- Push event: 12
- Pull request review comment event: 2
- Pull request review event: 3
- Pull request event: 9
- Fork event: 4
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| fhh2626 | f****6@g****m | 176 |
| hanatok | s****3@g****m | 37 |
| Nazanin | n****r@g****m | 1 |
Issues and Pull Requests
Last synced: 10 months ago
All Time
- Total issues: 55
- Total pull requests: 93
- Average time to close issues: 3 months
- Average time to close pull requests: 29 days
- Total issue authors: 27
- Total pull request authors: 6
- Average comments per issue: 2.38
- Average comments per pull request: 0.45
- Merged pull requests: 80
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 7
- Pull requests: 8
- Average time to close issues: 13 days
- Average time to close pull requests: 3 days
- Issue authors: 5
- Pull request authors: 4
- Average comments per issue: 0.0
- Average comments per pull request: 0.25
- Merged pull requests: 5
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- fhh2626 (8)
- shradheyagupta (6)
- bhavranek (4)
- groponp (4)
- ReneHamburger1993 (3)
- mglgc (2)
- almeida85 (2)
- ljh433 (2)
- Jiasheng321 (2)
- athebault67 (2)
- cadduser (2)
- Tangbbmc (2)
- gokulalgates (2)
- christos-efthymiou (1)
- purnawanpp (1)
Pull Request Authors
- fhh2626 (59)
- HanatoK (27)
- Tinkbian (4)
- giacomofiorin (1)
- ndonyapour (1)
- A-Frances (1)
Top Labels
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Packages
- Total packages: 2
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Total downloads:
- pypi 221 last-month
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Total dependent packages: 0
(may contain duplicates) -
Total dependent repositories: 1
(may contain duplicates) - Total versions: 39
- Total maintainers: 2
pypi.org: bfee2
Binding Free Energy Estimator 2
- Homepage: https://github.com/fhh2626/BFEE2
- Documentation: https://bfee2.readthedocs.io/
- License: GPLv3
-
Latest release: 3.0.0
published about 1 year ago
Rankings
conda-forge.org: bfee2
Binding free energy estimator (BFEE) is a python-based software that automates absolute binding free energy calculations through either the alchemical or geometric route by molecular dynamics simulations.
- Homepage: https://github.com/fhh2626/BFEE2
- License: GPL-3.0-or-later
-
Latest release: 2.3.1
published over 3 years ago