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af2_gpcr_kinase

A series of scripts that facilitate the prediction of user-defined protein structural properties using AlphaFold2

alphaflow

AlphaFold Meets Flow Matching for Generating Protein Ensembles

autodock-vina

AutoDock Vina

colabfold

Making Protein folding accessible to all!

diffdock

Implementation of DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking

diffusionproteinligand

dlpacker

DLPacker

dynamicbind

repo for DynamicBind: Predicting ligand-specific protein-ligand complex structure with a deep equivariant generative model

evo

DNA foundation modeling from molecular to genome scale

foldseek

Foldseek enables fast and sensitive comparisons of large structure sets.

kiheonbaek.github.io

kincore-standalone

ligandmpnn

ligprepper

Prepare a 3D SDF file from SMILES for a ligand

mmseqs2

MMseqs2: ultra fast and sensitive search and clustering suite

neuralplexer

NeuralPLexer: State-specific protein-ligand complex structure prediction with a multi-scale deep generative model

p2rank

P2Rank: Protein-ligand binding site prediction tool based on machine learning. Stand-alone command line program / Java library for predicting ligand binding pockets from protein structure.

pointsite

PointSite: a point cloud segmentation tool for identification of protein ligand binding atoms

proteinmpnn

Code for the ProteinMPNN paper

prottrans

ProtTrans is providing state of the art pretrained language models for proteins. ProtTrans was trained on thousands of GPUs from Summit and hundreds of Google TPUs using Transformers Models.

pseudocycle_small_molecule_binder

Small_molecule_binder_design_use_pseudocycles

reduce

Reduce - tool for adding and correcting hydrogens in PDB files

rosettafold-all-atom

umol

Protein-ligand structure prediction

uni-dock

Uni-Dock: a GPU-accelerated molecular docking program

vina-gpu-2.1

Vina-GPU 2.1, an improved docking toolkit for faster speed and higher accuracy on the virtual screening