JacobKMcPherson
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Molecular Dynamics (MD) and conformational ensembles
MDAnalysis is a Python library to analyze molecular dynamics simulations.
Public/backup repository of the GROMACS molecular simulation toolkit. Please do not mine the metadata blindly; we use https://gitlab.com/gromacs/gromacs for code review and issue tracking.
Neural networks for cryo-EM reconstruction
Amortized inference for ab initio heterogeneous cryo-EM reconstruction
Listing of papers about machine learning for proteins.
A series of scripts that facilitate the prediction of protein structures in multiple conformations using AlphaFold2
Predict multiple protein conformations using sequence clustering and AlphaFold2.
My progress in programming in Julia for Molecular Dynamics (a subject in the University)