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

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.

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

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](https://docs.anaconda.com/anaconda/install/). 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](https://pyplif-hippos.readthedocs.io/en/latest/getting-started-genref.html) and Getting Started tutorial for [AutoDock Vina](https://pyplif-hippos.readthedocs.io/en/latest/getting-started-vina.html) or [PLANTS](https://pyplif-hippos.readthedocs.io/en/latest/getting-started-plants.html). ## Ideas for Improvement? Found Bug(s)? If you have any idea for improvement or found bug to report feel free to write them [here](https://github.com/radifar/PyPLIF-HIPPOS/issues). ## 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](https://international.ristekdikti.go.id/) (Indonesia) under grant agreement No. 807.7/LL5/PG/2020. This project has been restructured based on the [MOLSSI Computational Molecular Science Python Cookiecutter](https://github.com/molssi/cookiecutter-cms) version 1.3, and benefited greatly from [MOLSSI Python Package Development Best Practices](https://molssi.org/2020/04/20/may-webinar-series-python-package-development/) workshop. ----- © Copyright 2021, Muhammad Radifar & Enade Perdana Istyastono