This repository contains code, data and tutarial for reproducing the paper "Machine Learning Coarse-Grained Potentials of Protein Thermodynamics". https://arxiv.org/abs/2212.07492
Proteins are the fundamental building blocks of life, and understanding their behavior is crucial for many applications in biology and biotechnology. Thermodynamics is a key tool for studying the behavior of proteins, but traditional methods for simulating protein thermodynamics can be computationally expensive and time-consuming.
Neural network potentials offer a promising alternative for simulating protein thermodynamics. By using machine learning techniques, we can train a neural network to predict the thermodynamic behavior of proteins based on their structure and other factors. This approach can be much faster and more efficient than traditional methods, and it can also provide more accurate results.
This repository contains the following:
To get started with this repository, follow these steps:
conda env create -f env.yml
Machine Learning Coarse-Grained Potentials of Protein Thermodynamics, https://doi.org/10.48550/arXiv.2212.07492
Note. All the code in this repository is MIT, however we use several file format readers that are taken from Moleculekit which has a free open source non-for-profit, research license. This is mainly in torchmd/run.py. Moleculekit is installed automatically being in the requirement file. Check out Moleculekit here: https://github.com/Acellera/moleculekit