Movements and confirmational changes within proteins are important for understanding protein function. Common methods for studying protein dynamics include molecular dynamics (MD) simulations and normal model analyses (NMA). Deep learning methods have also been applied to probe protein dynamics.
Table of contents
ProDy
A collection of tools for studying different aspects of protein dynamics. I am preparing a more detailed walkthrough, looking more closely at the structural dynamics of a crystal structure of terpene synthase (TPS). Updates will be included in the Bioinformatics tab.
https://academic.oup.com/bioinformatics/article-abstract/27/11/1575/217006
Instructions and documentation for the Python package:
http://prody.csb.pitt.edu
Making it rain
User-friendly front-end for running molecular dynamics (MD) simulations.
https://pubs.acs.org/doi/10.1021/acs.jcim.1c00998
Different Google colab notebooks available:
https://github.com/pablo-arantes/making-it-rain
Molecular Dynamics on Cloud Computing
Instructions for doing molecular dynamics on Google Compute Engine, AWS (Amazon Web Services), and other Cloud Computing services.
Short blog post:
https://www.tanerkaragol.com/post/molecular-dynamics-on-google-compute-engine-aws-amazon-web-services-and-other-cloud-computing-se
Instructions available at:
https://github.com/karagol-taner/Molecular-Dynamics-on-AWS-and-Cloud-Computing
Protein Conformation Prediction
Subsampled AF2
High-throughput prediction of protein conformational distributions with subsampled AlphaFold2
AFCluster
Predicting multiple conformations via sequence clustering and AlphaFold2
AF2Complex
AF2Complex predicts direct physical interactions in multimeric proteins with deep learning
StELa
Searching for Structure: Characterizing the Protein Conformational Landscape with Clustering-Based Algorithms
Af2 Conformations
Sampling alternative conformational states of transporters and receptors with AlphaFold2
Trajectory Analysis
mRMSD
Analysis of Protein Folding Simulation with Moving Root Mean Square Deviation