zackmawaldi

Frame2seq

Structure-conditioned masked language modeling for protein sequence design

upside2-md

torchmd-protein-thermodynamics

Tutorials and data necessary to reproduce the results of publication Machine Learning Coarse-Grained Potentials of Protein Thermodynamics

latent-gan

An implementation of the Latent Gan as discribed in the publication [cite]

making-it-rain

Cloud-based molecular simulations for everyone

MAGPIE

MAGPIE

dmol-book

Deep learning for molecules and materials book

Color-diffusion

A diffusion model to colorize black and white images

Machine-learning-for-proteins

Listing of papers about machine learning for proteins.

dl_binder_design

RFdiffusion

Code for running RFdiffusion

FragQuality

Measures the RMSD for each fragment at each protein structure's position and plots the lowest RMSD fragment for each position

NTF2Gen

NTF2Gen: An enumerative algorithm for generating full-atom models of proteins belonging to the NTF2-like superfamily

parametric_scaffold_design

PyRosetta scripts for parametric protein scaffold design

metal-site-prediction

RFDesign

Protein hallucination and inpainting with RoseTTAFold

donut_protein_manuscript

code used in our manuscript: De novo design of protein homodimers containing tunable symmetric protein pockets

ProteinMPNN

Code for the ProteinMPNN paper

twitch-dl

CLI tool for downloading videos from Twitch.