amdock
(Linux and macOS) AMDock: Assisted molecular docking with AutoDock4 and AutoDockVina
Science Score: 13.0%
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○CITATION.cff file
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✓DOI references
Found 4 DOI reference(s) in README -
○Academic publication links
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○Scientific vocabulary similarity
Low similarity (16.2%) to scientific vocabulary
Keywords
Repository
(Linux and macOS) AMDock: Assisted molecular docking with AutoDock4 and AutoDockVina
Basic Info
Statistics
- Stars: 70
- Watchers: 4
- Forks: 19
- Open Issues: 12
- Releases: 3
Topics
Metadata Files
README.md
AMDock: Assisted Molecular Docking with Autodock4 and Autodock Vina
AMDock (Assisted Molecular Docking) is a user-friendly graphical tool to assist in the docking of protein-ligand complexes using Autodock-Vina or AutoDock4. This tool integrates several external programs for processing docking input files, define the search space (box) and perform docking under user’s supervision.
Version 1.6.x for Linux (Build 1.6.1-beta)
DOCUMENTATION
Manual, tutorials and test files are located in Doc folder. (May be out of date. Please check the wiki)
Cite us
Valdes-Tresanco, M.S., Valdes-Tresanco, M.E., Valiente, P.A. and Moreno E. AMDock: a versatile graphical tool for assisting molecular docking with Autodock Vina and Autodock4. Biol Direct 15, 12 (2020). https://doi.org/10.1186/s13062-020-00267-2
INSTALL
Installation can be carried out in two ways 1. (For Linux only) Using a conda environment.
Note: macOS users can use this procedure, however, PyMOL must be compiled using this environment's Python interpreter, since there is no working version of PyMOL for mac in the anaconda repositories.
To do this, proceed as follows:
If you don't have conda installed, please visit the Miniconda download page.
Those with an existing conda installation may wish to create a new conda "environment" to avoid conflicts with what you already have installed. To do this:
conda create --name AMDock python=3.9
conda activate AMDock
(Note that you would need to perform the "conda activate" step every time you wish to use AMDock in a new terminal; it might be appropriate to add this to your start-up script. Creating a new environment should not be necessary if you only use conda for AMDock.)
Once this is done, type:
conda install -c conda-forge pymol-open-source openbabel pdb2pqr
and finally:
python -m pip install git+https://github.com/Valdes-Tresanco-MS/AutoDockTools_py3 PyQt5
python -m pip install AMDock
Using the OS Python 3 environment. To do this, proceed as follows:
sudo apt install pymol openbabel
(Note that this version of AMDock works with openbabel 3.x)
python3 -m pip install pdb2pqr PyQt5
python3 -m pip install git+https://github.com/Valdes-Tresanco-MS/AutoDockTools_py3
python3 -m pip install AMDock
Before using AMDock, you most install the PyMOL plugin (grid_amdock.py).
If it does not appear please follow the instructions: - Download the gridamdock.py file - Open PyMOL > Plugins > Manager Plugins > Install New Plugin > Choose File and select the gridamdock.py file - Restart PyMOL
To open AMDock, type in the terminal:
AMDock
Note: You can add this line to the .bashrc file to activate de AMDock conda environment and execute AMDock directly
alias amdock="conda activate AMDock; AMDock"
For macOS users,
To view the update history, please check Changes_History file
TUTORIALS
Please, check the wiki https://github.com/Valdes-Tresanco-MS/AMDock-win/wiki
Support
This project is possible thanks to the Open Source license of the JetBrains programs.
Owner
- Name: Mario Sergio Valdés Tresanco
- Login: Valdes-Tresanco-MS
- Kind: user
- Location: Colombia
- Company: University of Medellín
- Repositories: 19
- Profile: https://github.com/Valdes-Tresanco-MS
P.h.D. in Modeling and Scientific Computing
GitHub Events
Total
- Issues event: 2
- Watch event: 9
- Issue comment event: 1
- Fork event: 2
Last Year
- Issues event: 2
- Watch event: 9
- Issue comment event: 1
- Fork event: 2
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Mario Sergio Valdés Tresanco | m****5@g****m | 275 |
| Valdes-Tresanco-MS | 3****S | 20 |
| Mario E. Valdes-Tresanco | 4****s | 4 |
| mario | m****a | 2 |
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 28
- Total pull requests: 5
- Average time to close issues: 7 months
- Average time to close pull requests: 1 minute
- Total issue authors: 22
- Total pull request authors: 1
- Average comments per issue: 2.32
- Average comments per pull request: 0.0
- Merged pull requests: 5
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 2
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 2
- Pull request authors: 0
- Average comments per issue: 0.5
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- Valdes-Tresanco-MS (3)
- houdini69 (2)
- debanjansen48 (2)
- truatpasteurdotfr (2)
- marioernestovaldes (2)
- Narsil-A (1)
- about0blank (1)
- seal28 (1)
- hima111997 (1)
- avinashkarkada (1)
- jhh1492 (1)
- drbenedictpaul (1)
- Ramstein (1)
- Oxeda (1)
- galeo (1)
Pull Request Authors
- Valdes-Tresanco-MS (5)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- pypi 91 last-month
- Total dependent packages: 0
- Total dependent repositories: 1
- Total versions: 2
- Total maintainers: 1
pypi.org: amdock
AMDock: Assisted Molecular Docking with Autodock4 and Autodock Vina
- Homepage: https://github.com/Valdes-Tresanco-MS/AMDock
- Documentation: https://amdock.readthedocs.io/
- License: GPLv3
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Latest release: 1.6.2
published about 4 years ago
Rankings
Maintainers (1)
Dependencies
- PyQt5 >=5.15.4