eunos-1128

se3-transformer-public

code for the SE3 Transformers paper: https://arxiv.org/abs/2006.10503

RoseTTAFold-All-Atom

rf_diffusion_all_atom

Public RFDiffusionAA repo

CombFold

ftdmp

FTDMP is a software system for running docking experiments and scoring/ranking multimeric models.

AF_unmasked

Source code and examples for AlphaFold Unmasked

chroma

A generative model for programmable protein design

MULTICOM3

The software system of improving AlphaFold2- and AlphaFold-Multimer-based protein tertiary & quaternary structure prediction. It was developed by the Bioinformatics and Machine Learning Lab at the University of Missouri. It was blindly tested in CASP15 and ranked among the best server predictors in 2022. It improves AlphaFold's accuracy by 5-10%.

MMGX

MMGX: Multiple Molecular Graph eXplainable Discovery

gms_natcomms_1705932980_data

Data sharing for High-throughput Prediction of Changes in Protein Conformational Distributions with Subsampled AlphaFold2

apex

A PyTorch Extension: Tools for easy mixed precision and distributed training in Pytorch

deepfold

Protein 3D Structure Prediction with DeepFold

DeepSpeed

DeepSpeed is a deep learning optimization library that makes distributed training and inference easy, efficient, and effective.

foldseek

Foldseek enables fast and sensitive comparisons of large structure sets.

protwis

Protwis is the backbone of the GPCRdb. The GPCRdb contains reference data, interactive visualisation and experiment design tools for G protein-coupled receptors (GPCRs).

ivy

Convert Machine Learning Code Between Frameworks

einops

Flexible and powerful tensor operations for readable and reliable code (for pytorch, jax, TF and others)

Uni-Dock

Uni-Dock: a GPU-accelerated molecular docking program

openmm

OpenMM is a toolkit for molecular simulation using high performance GPU code.

pdbfixer

PDBFixer fixes problems in PDB files

AutoDock-GPU

AutoDock for GPUs and other accelerators

AutoDock4

AutoGrid

scrubber

Enumerate conformational, protomeric, and pH-related microstates for docking with AutoDock

waterkit

Tool to predict water molecules placement and energy in ligand binding sites

Ringtail

Package for storage and analysis of virtual screenings run with AutoDock-GPU and AutoDock Vina

pdb-tools

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

weko

Weko3 is a repository software based on inveno3.

cctbx_project

Computational Crystallography Toolbox

nbopen

Open a Jupyter notebook in the best available server