Metadata-Version: 2.1
Name: BFEE2
Version: 2.3.0
Summary: Binding Free Energy Estimator 2
Home-page: https://github.com/fhh2626/BFEE2
Author: Haohao Fu, Haochuan Chen, Wensheng Cai and Chris Chipot
Author-email: wscai@nankai.edu.cn
Maintainer: Haohao Fu
Maintainer-email: fhh2626@mail.nankai.edu.cn
License: GPLv3
Platform: UNKNOWN
Requires-Python: >=3.6
Description-Content-Type: text/markdown
License-File: LICENSE

# Binding Free Energy Estimator 2
[![DOI](https://zenodo.org/badge/322234705.svg)](https://zenodo.org/badge/latestdoi/322234705)

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.<br>

## 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](https://pubs.acs.org/doi/abs/10.1021/jp0217839). 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](https://pubs.acs.org/doi/abs/10.1021/acs.jctc.7b00791) for introduction of these variables.<br>

In the [geometric route](https://pubs.acs.org/doi/10.1021/ct3008099), the degrees of freedom is investigated one by one, through one-dimensional free-energy calculations. In BFEE, [WTM-eABF](https://pubs.acs.org/doi/abs/10.1021/acs.accounts.9b00473) is used, while other importance-sampling algorithms such as [plain eABF](https://pubs.acs.org/doi/abs/10.1021/acs.jctc.6b00447) are also acceptable.
The [alchemical route](https://pubs.acs.org/doi/10.1021/ct3008099) is a variants of the [double decoupling method (DDM)](https://www.sciencedirect.com/science/article/pii/S0006349597787563). A thermodynamic cycle, in which the ligand and the geometric restraints are decoupled independently to guarantee the convergence of the simulations.<br>
[这里](http://sioc-journal.cn/Jwk_hxxb/CN/10.6023/A20100489)是标准结合自由能计算方法的中文介绍.<br>

## Features
Generates all the input files for absolute binding free energy calculations;<br>
Perform post-treatment automatedly;<br>
Support NAMD (alchemical and geometric route) and Gromacs (geometric route) as molecular dynamics engines;<br>
Support many file formats for the input complex structure (PSF/PDB/PRM, PRM7/RST7, TOP/PDB);<br>
...<br>

## Requirements
Python 3.6+, PySide 2, numpy, matplotlib and MDAnalysis.<br>
[NAMD 3.0 or later](https://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=NAMD) / [Colvars patched Gromacs](https://github.com/Colvars/colvars).<br>

## Installation
We suggest to install BFEE2 through conda. It will be safe if conda is install in a new environment<br>
```
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.<br>
A step-by-step tutorial is provided [here](https://www.nature.com/articles/s41596-021-00676-1).<br>

## Citations
When possible, please consider mentioning [Fu et al. Nat. Protoc. 2022, doi:10.1038/s41596-021-00676-1](https://www.nature.com/articles/s41596-021-00676-1#citeas) when BFEE2 is used in your project.


Additional references:<br>
BFEE2: [Fu et al. J. Chem. Inf. Model. 2021, 61, 2116–2123](https://pubs.acs.org/doi/abs/10.1021/acs.jcim.1c00269)<br>
Alchemical and geometric routes [Gumbart et al. J. Chem. Theory Comput. 2013, 9, 794–802](https://pubs.acs.org/doi/abs/10.1021/ct3008099)<br>
WTM-eABF: [Fu et al. Acc. Chem. Res. 2019, 52, 3254–3264](https://pubs.acs.org/doi/abs/10.1021/acs.accounts.9b00473) and [Fu et al. J. Phys. Chem. Lett. 2018, 9, 4738–4745](https://pubs.acs.org/doi/abs/10.1021/acs.jpclett.8b01994)<br>
Collective variables: [Fu et al. J. Chem. Theory Comput. 2017, 13, 5173–5178](https://pubs.acs.org/doi/abs/10.1021/acs.jctc.7b00791)<br>
Colvars module: [Fiorin et al. Mol. Phys. 2013 111, 3345-3362](https://www.tandfonline.com/doi/full/10.1080/00268976.2013.813594)<br>
"Mother" of all restraint-based binding free-energy calculations: [Hermans et al. Isr. J. Chem. 1986, 27, 225–227](https://onlinelibrary.wiley.com/doi/abs/10.1002/ijch.198600032)<br>

## Contact us
Technique issues: Haohao Fu (fhh2626@mail.nankai.edu.cn) and Haochuan Chen (yjcoshc@mail.nankai.edu.cn)<br>

This software is under the [GPLv3](https://www.gnu.org/licenses/gpl-3.0.en.html) license. For more information about the copyright of BFEE, contact the corresponding authors of the aforementioned papers (wscai@nankai.edu.cn, Christophe.Chipot@univ-lorraine.fr).


