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mdpertool

Perturbation based Allosteric Pathway Finder

https://github.com/bio-otto/mdpertool_gui

Science Score: 41.0%

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
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    1 of 3 committers (33.3%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (12.8%) to scientific vocabulary
Last synced: 10 months ago · JSON representation ·

Repository

Perturbation based Allosteric Pathway Finder

Basic Info
  • Host: GitHub
  • Owner: Bio-Otto
  • License: mit
  • Language: Python
  • Default Branch: master
  • Size: 252 MB
Statistics
  • Stars: 6
  • Watchers: 2
  • Forks: 1
  • Open Issues: 0
  • Releases: 2
Created over 5 years ago · Last pushed over 1 year ago
Metadata Files
Readme Changelog License Citation

README.md

MDPERTOOL: Perturbation-based Allosteric Pathway Finder

Conda Build Platforms Download Counter License GitHub contributors website Twitter Follow Stars Badge Forks Badge

A Software Tool for Investigation of Allosteric Communication within Protein Structures via Energy Dissipation in Molecular Dynamics Simulations

MDPerTool Animation

📥 Installation

To install MDPERTOOL using Conda, simply run the following commands:

sh conda install bio-otto::mdpertool This will install MDPERTOOL and all of its dependencies. Once the installation is completed, you can access the Command Line Interface by typing 'mdpertool' in your terminal.

Manual Installation

To manually install MDPERTOOL, follow the instructions below:

For Windows Users

cmd git clone https://github.com/Bio-Otto/MDPerTool_GUI.git cd MDPerTool_GUI conda env create -f envs/winx64_env.yml conda activate mdpertool cd mdpertool python ui_main.py

For Linux Users

sh git clone https://github.com/Bio-Otto/MDPerTool_GUI.git cd MDPerTool_GUI conda env create -f envs/linux64_env.yml conda activate mdpertool cd mdpertool python ui_main.py

🖥️ Terminal Usage

For terminal usage, run:

sh python no_gui.py -p pdb_file -wdcd True -pert_res 'SER345' -speed_factor 4

📦 Dependencies

  • OpenMM - A high performance toolkit for molecular simulation.

  • Networkx - NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks.

  • Pandas - pandas is a fast, powerful, flexible and easy to use open source data analysis and manipulation tool

  • Numpy - The fundamental package for scientific computing with Python

  • Pymol (Open Source) - PyMOL is a user-sponsored molecular visualization system on an open-source foundation, maintained and distributed by Schrödinger.

  • Matplotlib - Matplotlib is a comprehensive library for creating static, animated, and interactive visualizations in Python.

  • Pyqtgraph - Scientific Graphics and GUI Library for Python

  • PySide2 - Python bindings for the Qt cross-platform application and UI framework

  • ProDy - Protein Dynamics and Sequence Analysis

  • Parmed - Parameter/topology editor and molecular simulator

And of course MDPERTOOL itself is an open source public repository.

Also you can check full functional parameters with:

sh python no_gui.py -h

For Molecular Dynamic Simulation production

sh python no_gui.py -p <pdb file> -pff <charmm36> -wff <tip5p> -wdcd <True>

MDPerTool applies Energy Dissipation Concept using OpenMM Molecular Dynamic Toolkit, which also supports the CUDA platform.

✨ Features

  • Automated topology builder
  • Residue base energy decomposition
  • DCD and XTC file format support
  • Easy to installation using Conda

Features of MDPERTOOL v0.0.1

This version of mdpertool includes the following features.

Feature Documentation
Each Residue Decomposition [plugins/dropbox/README.md][MDPERTOOL]
Molecular Dynamic Simulation [plugins/github/README.md][MDPERTOOL]
Energy Dissipation Network [plugins/googledrive/README.md][MDPERTOOL]
Free Energy Calculations [plugins/onedrive/README.md][MDPERTOOL]

🚀 Development

Want to contribute? Get a branch and join us to make MDPERTOOL even greater!

📋 Todos

  • Write MORE Tests
  • Add Light Mode

📝 License

MDPERTOOL is licensed under the MIT License. See the LICENSE file for more details.

Free Software, Hell Yeah!

Owner

  • Name: HIbrahim
  • Login: Bio-Otto
  • Kind: user
  • Location: Göztepe/Kadıköy/İstanbul
  • Company: Marmara University/ Computational Biology and Bioinformatics Lab

focuses on applying atomistic molecular simulation methods to complex problems in biology and human health

Citation (CITATION.md) 

# Citation of UConnRCMPy

[![DOI](https://zenodo.org/badge/36095263.svg)](https://zenodo.org/badge/latestdoi/36095263)

To cite UConnRCMPy in a scholarly article, please use

> B. W. Weber, R. Fang, and C.J. Sung. (2017) UConnRCMPy v3.0.2 [software]. Zenodo. https://doi.org/10.5281/zenodo.594918

A BibTeX entry for LaTeX users is

```TeX
@software{uconnrcmpy,
  title = {{{UConnRCMPy}}},
  url = {https://github.com/bryanwweber/UConnRCMPy},
  version = {3.0.3},
  author = {Weber, Bryan William and Fang, Ruozhou and Sung, Chih-Jen},
  date = {2017-04},
  doi = {10.5281/zenodo.594918}
}
```

The DOI for the latest version can be found in the badge at the top.
If you would like to cite a specific, older version, the DOIs for each release are:

 * v3.0.4: [10.5281/zenodo.815568](https://doi.org/10.5281/zenodo.815568)
 * v3.0.3: [10.5281/zenodo.810181](https://doi.org/10.5281/zenodo.810181)
 * v3.0.2: [10.5281/zenodo.556469](https://doi.org/10.5281/zenodo.556469)
 * v3.0.1: [10.5281/zenodo.321427](https://doi.org/10.5281/zenodo.321427)
 * v3.0.0: [10.5281/zenodo.269678](https://doi.org/10.5281/zenodo.269678)

GitHub Events

Total
  • Push event: 2
Last Year
  • Push event: 2

Committers

Last synced: over 3 years ago

All Time
  • Total Commits: 284
  • Total Committers: 3
  • Avg Commits per committer: 94.667
  • Development Distribution Score (DDS): 0.437
Top Committers
Name Email Commits
HIbrahim 5****o@u****m 160
HIbrahim h****r@g****m 122
bio-otto h****7@m****r 2
Committer Domains (Top 20 + Academic)
marun.edu.tr: 1

Issues and Pull Requests

Last synced: almost 2 years ago

All Time
  • Total issues: 0
  • Total pull requests: 3
  • Average time to close issues: N/A
  • Average time to close pull requests: 16 days
  • Total issue authors: 0
  • Total pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 3
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 1
  • Average time to close issues: N/A
  • Average time to close pull requests: 4 minutes
  • Issue authors: 0
  • Pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
Pull Request Authors
  • Bio-Otto (2)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 13 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 3
  • Total maintainers: 1
pypi.org: mdpertool

A Software Tool for Investigation of Allosteric Communication within Protein Structures via Energy Dissipation in Molecular Dynamics Simulations

  • Versions: 3
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 13 Last month
Rankings
Dependent packages count: 10.1%
Dependent repos count: 21.5%
Forks count: 22.6%
Stargazers count: 23.1%
Average: 27.2%
Downloads: 58.7%
Maintainers (1)
bio-otto
Last synced: 10 months ago

Dependencies

pyproject.toml pypi
setup.py pypi