joelmeyerson

alignment-server

Simple server to translate input DNA to a peptide and search genomes for a parent protein.

autopick-bc

Image classification module for protein detection in cryo-EM data.

conformation-inspector

Python script to visualize statistics on the conformational composition of protein oligomers in cryo-EM data.

cryobase

React/Electron desktop app for managing cryo-electron microscopy data on AWS S3.

ctf-grapher

Graphical tool to visualize the contrast transfer function (CTF) of an electron microscope.

dllogger

A logging tool for deep learning.

esm

Evolutionary Scale Modeling (esm): Pretrained language models for proteins

EVcouplings

Evolutionary couplings from protein and RNA sequence alignments

flash-attention

Fast and memory-efficient exact attention

genie

De Novo Protein Design by Equivariantly Diffusing Oriented Residue Clouds

hole-cmm

Python script to convert HOLE program output to Chimera and ChimeraX marker files.

quick-montage

Generate a montage of a cryo-EM image with its associated power spectrum and CTF estimate.

LigandMPNN

openfold

Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2

plmc

Inference of couplings in proteins and RNAs from sequence variation

ProteinMPNN

Code for the ProteinMPNN paper

RoseTTAFold-All-Atom