Molecular Kinetics via Topology

2024/12/29 by Surahit Chewle, Donati, Luca, Dominik St. Pierre +6 · 1 citation
Biochemistry, Genetics and Molecular Biology · Medicine · #Bioinformatics and Genomic Networks #Microbial Natural Products and Biosynthesis #ATP Synthase and ATPases Research

paper · pdf · doi:10.48550/arxiv.2412.20580

Abstract

MoKiTo (Molecular Kinetics via Topology) is a Python-based toolkit designed for analyzing and extracting topological insights from Molecular Dynamics (MD) simulations.It enables researchers to study conformational transitions and kinetic pathways in molecular systems by generating Molecular Kinetics Maps (MKMs). This package contains contains the complete dataset (software code, input data and output data) of the examples described in the article ``Topological analysis reveals multiple pathways in molecular dynamics'' by Luca Donati, Surahit Chewle, Dominik St. Pierre, Vijay Natarajan and Marcus Weber. The software code is also available on GITHUB.

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