domgutier

deepmind-research

This repository contains implementations and illustrative code to accompany DeepMind publications

openfold

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

alphafold_pytorch

An implementation of the DeepMind's AlphaFold based on PyTorch for research

pdb-tools

A dependency-free cross-platform swiss army knife for PDB files.

cryodrgn

Neural networks for cryo-EM reconstruction

EVcouplings

Evolutionary couplings from protein and RNA sequence alignments

rna-tools

🔧rna-tools: a toolbox to analyze sequences, structures and simulations of RNA (and more) used by RNA CASP, RNA PUZZLES, and me ;-) docs @ http://rna-tools.rtfd.io web @ http://rna-tools.online

learn_cryoem_math

DMPfold

De novo protein structure prediction using iteratively predicted structural constraints

deepEMhancer

Deep learning for cryo-EM maps post-processing

haddock-tools

Set of useful HADDOCK utility scripts

starfile

STAR file I/O in Python

qfit-3.0

qFit: Automated and unbiased multi-conformer models from X-ray and EM maps.

pae_to_domains

Graph-based community clustering approach to extract protein domains from a predicted aligned error matrix

gP2S

A laboratory information management system (LIMS) for cryoEM

dynamo2m

a bidirectional interface between Dynamo and the Warp-RELION-M pipeline

ManifoldEM_Python

ManifoldEM Python suite

MRC_napari_viewer

Cryo-EM data viewer in napari

protlego

Automated construction of protein chimeras and their analysis.

CryoGridTools

3D printing data in "Tidy up cryo-EM sample grids with 3D printed tools"

CryoEM-scripts

Badly written scripts for making cryoEM easier

omnia-md

LocSpiral-LocBSharpen-LocBFactor-LocOccupancy

Local computational methods to improve the interpretability and analysis of cryo-EM maps

SamplingGui

GUI for analyzing Fourier space sampling in cryo-EM

coconet

RNA Contact Prediction Using Coevolution and Convolutional Neural Network

BIUcontrol

Software to control the Back It Up device

SIOcontrol

SIO device control

cyoEMtools

cyoEM tools

coldboxwatcher

grid-freezing-components

3D printed and CNC milled components for home built grid freezing devices