Standardized data set for machine learning of protein structure

EquiBind: geometric deep learning for fast predictions of the 3D structure in which a small molecule binds to a protein

Toolbox for molecular animations in Blender, powered by Geometry Nodes.

A Python API for the RCSB Protein Data Bank (PDB)

EquiDock: geometric deep learning for fast rigid 3D protein-protein docking

A PyTorch framework for prediction of tertiary protein structure

Diffusion models of protein structure; trigonometry and attention are all you need!

MoleculeKit: Your favorite molecule manipulation kit

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.

Official repo of the modular BioExcel version of HADDOCK

Implementation of Protein Classification based on subcellular localization using ProtBert(Rostlab/prot_bert_bfd_localization) model from Hugging Face library, based on BERT model trained on large corpus of protein sequences.

Python macromolecular parsing (with .pdb/.cif/.mmtf parsing and production)

Bio4j abstract model and general entry point to the project

R client for the OmniPath web service

Application to assign secondary structure to proteins

Mutual Information Tools for protein Sequence analysis in Julia

Implementation and replication of ProGen, Language Modeling for Protein Generation, in Jax

Detailed nutrient composition of 528 key foods in India.

The pmartR R package provides functionality for quality control, normalization, exploratory data analysis, and statistical analysis of mass spectrometry (MS) omics data, in particular proteomic (either at the peptide or the protein level), lipidomic, and metabolomic data.

Official code repository for EquiFold: Protein Structure Prediction with a Novel Coarse-Grained Structure Representation