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pyplif-hippos

HIPPOS Is PyPLIF On Steroids. A Molecular Interaction Fingerprinting Tool for Docking Results of Autodock Vina and PLANTS

https://github.com/radifar/pyplif-hippos

Science Score: 67.0%

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    Low similarity (12.4%) to scientific vocabulary

Keywords

autodock-vina drug-discovery interaction-fingerprinting molecular-docking virtual-screening
Last synced: 6 months ago · JSON representation ·

Repository

HIPPOS Is PyPLIF On Steroids. A Molecular Interaction Fingerprinting Tool for Docking Results of Autodock Vina and PLANTS

Basic Info
Statistics
  • Stars: 29
  • Watchers: 4
  • Forks: 8
  • Open Issues: 4
  • Releases: 4
Topics
autodock-vina drug-discovery interaction-fingerprinting molecular-docking virtual-screening
Created over 5 years ago · Last pushed over 2 years ago
Metadata Files
Readme License Code of conduct Citation

README.md

PyPLIF HIPPOS: A Molecular Interaction Fingerprinting Tool for Docking Results of AutoDock Vina and PLANTS

GitHub Actions Build Status Language grade: Python codecov
Anaconda-Server Badge Documentation Status DOI:10.1021/acs.jcim.0c00305
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Icons made by Freepik from Flaticon is licensed by CC 3.0 BY

Icons made by Freepik from Flaticon is licensed by CC 3.0 BY

Welcome to PyPLIF-HIPPOS's project page. PyPLIF-HIPPOS is an upgraded version of PyPLIF (Python-based Protein-Ligand Interaction Fingerprinting), a tool for molecular docking post-analysis. It will translate the 3D coordinates of both ligand(s) (generated from docking simulation) and protein into a series of interaction bitstring (also known as Interaction Fingerprint) (see image below). HIPPOS (/ˌhipoʊz/) is a recursive acronym of HIPPOS Is PyPLIF On Steroids. From this point forward, PyPLIF-HIPPOS is simplified to HIPPOS.

Compared to PyPLIF, HIPPOS is not only faster and able to generate more customized interaction bitstring, but also supports both PLANTS & Vina! More over, unlike its predecessor it is (far) more well-documented.

Table of Content Abstract Graphic JCIM

Reprinted with permission from https://doi.org/10.1021/acs.jcim.0c00305. Copyright 2020 American Chemical Society.

PyPLIF output from PyPLIF publication

Illustration by Radifar et al (2013) from Bioinformation.net is licensed by CC 4.0 BY

Quick Installation

The easiest way to install HIPPOS is using Anaconda or Miniconda. If you have Anaconda or Miniconda ready in your machine, you can start with creating new environment (recommended):

conda create -n hippos python=3.6

Then activate the environment and install HIPPOS:

conda activate hippos
conda install -c conda-forge pyplif-hippos

next you can try run HIPPOS and HIPPOS-GENREF with the following command:

hippos
hippos-genref

How to Use HIPPOS

So I already installed HIPPOS, now what? Well you could start with how to generate the reference bitstring and Getting Started tutorial for AutoDock Vina or PLANTS.

Ideas for Improvement? Found Bug(s)?

If you have any idea for improvement or found bug to report feel free to write them here.

Citing HIPPOS

If you are using HIPPOS please cite this paper:

Istyastono, E., Radifar, M., Yuniarti, N., Prasasty, V. and Mungkasi, S., 2020. PyPLIF HIPPOS: A Molecular Interaction Fingerprinting Tool for Docking Results of AutoDock Vina and PLANTS. Journal of Chemical Information and Modeling, 60(8), pp.3697-3702. https://doi.org/10.1021/acs.jcim.0c00305

Acknowledgment

This project has received funding from the National Agency for Research and Innovation (Indonesia) under grant agreement No. 807.7/LL5/PG/2020. This project has been restructured based on the MOLSSI Computational Molecular Science Python Cookiecutter version 1.3, and benefited greatly from MOLSSI Python Package Development Best Practices workshop.

© Copyright 2021, Muhammad Radifar & Enade Perdana Istyastono

Owner

  • Name: Muhammad Radifar
  • Login: radifar
  • Kind: user
  • Location: Yogyakarta, Indonesia
  • Company: PICompS

Independent Researcher. Computational Chemist, Software Engineer, Full Stack Developer (Django, Vue, GraphQL). ❤ QM/MM & Enzyme Design.

Citation (CITATION.cff) 

# YAML 1.2
---
abstract: "We describe here our tool named PyPLIF HIPPOS, which was newly developed to analyze the docking results of AutoDock Vina and PLANTS. Its predecessor, PyPLIF (https://github.com/radifar/pyplif), is a molecular interaction fingerprinting tool for the docking results of PLANTS, exclusively. Unlike its predecessor, PyPLIF HIPPOS speeds up the computational times by separating the reference generation and docking analysis. PyPLIF HIPPOS also offers more options compared to PyPLIF. PyPLIF HIPPOS for Linux is stored as the Supporting Information in this application note and can be accessed in GitHub (https://github.com/radifar/PyPLIF-HIPPOS). Additionally, we present here the application of the tool in a retrospective structure-based virtual screening campaign targeting neuraminidase."
authors: 
  -
    affiliation: "Faculty of Pharmacy, Sanata Dharma University"
    family-names: Istyastono
    given-names: "Enade Perdana"
    orcid: "https://orcid.org/0000-0002-8344-5587"
  -
    affiliation: "Center for Molecular Modeling (molmod.org)"
    family-names: Radifar
    given-names: Muhammad
    orcid: "https://orcid.org/0000-0001-9156-9478"
  -
    affiliation: "Department of Pharmacology and Clinical Pharmacy, Faculty of Pharmacy, Universitas Gadjah Mada"
    family-names: Yuniarti
    given-names: Nunung
    orcid: "https://orcid.org/0000-0002-4500-6065"
  -
    affiliation: "Faculty of Biotechnology, Atma Jaya Catholic University of Indonesia"
    family-names: Prasasty
    given-names: "Vivitri Dewi"
    orcid: "https://orcid.org/0000-0002-2992-1247"
  -
    affiliation: "Department of Mathematics, Faculty of Science and Technology, Sanata Dharma University"
    family-names: Mungkasi
    given-names: Sudi
    orcid: "https://orcid.org/0000-0001-5319-9744"
cff-version: "1.1.0"
date-released: 2020-07-20
doi: "10.1021/acs.jcim.0c00305"
message: "If you use this software, please cite it using these metadata."
repository-code: "https://github.com/radifar/PyPLIF-HIPPOS"
title: "PyPLIF-HIPPOS"
version: "0.1.2"
...

GitHub Events

Total
  • Issues event: 2
  • Watch event: 1
Last Year
  • Issues event: 2
  • Watch event: 1

Committers

Last synced: almost 3 years ago

All Time
  • Total Commits: 238
  • Total Committers: 2
  • Avg Commits per committer: 119.0
  • Development Distribution Score (DDS): 0.013
Past Year
  • Commits: 12
  • Committers: 1
  • Avg Commits per committer: 12.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
radifar m****5@g****m 235
dependabot[bot] 4****]@u****m 3

Issues and Pull Requests

Last synced: 8 months ago

All Time
  • Total issues: 3
  • Total pull requests: 9
  • Average time to close issues: N/A
  • Average time to close pull requests: 28 days
  • Total issue authors: 3
  • Total pull request authors: 2
  • Average comments per issue: 0.33
  • Average comments per pull request: 0.67
  • Merged pull requests: 8
  • Bot issues: 0
  • Bot pull requests: 4
Past Year
  • Issues: 1
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 1
  • Pull request authors: 0
  • Average comments per issue: 1.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
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Top Authors
Issue Authors
  • rezkirasyak (1)
  • EmanuelD1989 (1)
  • chenbq18 (1)
Pull Request Authors
  • radifar (5)
  • dependabot[bot] (4)
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dependencies (4)

Packages

  • Total packages: 2
  • Total downloads:
    • pypi 11 last-month
  • Total dependent packages: 0
    (may contain duplicates)
  • Total dependent repositories: 1
    (may contain duplicates)
  • Total versions: 4
  • Total maintainers: 1
pypi.org: pyplif-hippos
  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 11 Last month
Rankings
Dependent packages count: 10.0%
Forks count: 11.9%
Stargazers count: 12.6%
Average: 20.9%
Dependent repos count: 21.8%
Downloads: 48.2%
Maintainers (1)
mradifar
Last synced: 6 months ago
conda-forge.org: pyplif-hippos

A Molecular Interaction Fingerprinting Tool for Docking Results of Autodock Vina and PLANTS.

  • Versions: 3
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent repos count: 34.0%
Average: 43.7%
Forks count: 44.7%
Stargazers count: 44.9%
Dependent packages count: 51.2%
Last synced: 6 months ago

Dependencies

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