{"repo":"fazekaszs/loco_hd","free":true,"listed":false,"github":"https://github.com/fazekaszs/loco_hd","clone":"git clone https://github.com/fazekaszs/loco_hd.git","description":"The LoCoHD metric for protein-protein structure comparison","language":"Python","stars":15,"topics":["bioinformatics","cheminformatics","metrics","molecular-modeling","structural-biology"],"license":"MIT","category":"analytics","readme_excerpt":"Welcome to LoCoHD ! LoCoHD ( Local Composition Hellinger Distance ) is a metric for comparing protein structures. It can be used for one single structure-structure comparison, for the comparison of multiple structures inside ensembles, or for the comparison of structures inside an MD simulation trajectory. It is also a general-purpose metric for labelled point clouds with variable point counts. In contrast to RMSD, the TM-score, lDDT, or GDT TS, it is based on the measurement of local composition differences, rather than of the Euclidean deviations. Where can I read about it? This work has been published in Nature Communications. If you would like to cite us, you can do it like this: Demo scripts If you are interested in how to run the Python scripts that are used for the creation of the article, see the PY SCRIPTS.md file. System requirements Software dependencies LoCoHD is a Python3 package, so it most definitely requires Python3. Additionally, it also needs BioPython and Numpy. It was tested with - Python version 3.10.10, - BioPython version 1.81, - Numpy version 1.21.6. Its build-dependencies are Rust (tested with rustc version 1.70.70) and Maturin (tested with version 0.14.15). Some of the scripts in python codes use other packages too: - Matplotlib version 3.7.1 - SciPy version 1.10.0 - MDAnalysis version 2.4.2 - scikit-learn version 1.2.1 The full package and scripts were tested on Linux (Pop! OS 22.04 LTS). Installation was tested on Pop! OS and OpenSUSE Leap 15.3. Ha","default_branch":null,"files":null,"tree":[],"storefront":"/r/fazekaszs","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/fazekaszs/loco_hd/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}