proteins

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

Standardized data set for machine learning of protein structure

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

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

P2Rank: Protein-ligand binding site prediction from protein structure based on machine learning.

PROPKA predicts the pKa values of ionizable groups in proteins and protein-ligand complexes based in the 3D structure.

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

Official repo of the modular BioExcel version of HADDOCK

Application to assign secondary structure to proteins

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

MoleculeKit: Your favorite molecule manipulation kit

Learning Universal Representations of Intermolecular Interactions with ATOMICA

A PyTorch framework for prediction of tertiary protein structure

R client for the OmniPath web service

sensitive and precise assembly of short sequencing reads

Open source biolab

A collection of resources for Deep Learning in Python for Life Sciences (with focus on biotech and pharma).

Notebooks to follow along with "Deep Learning for Biology" Chapters 2 to 6.

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

Geom3D: Geometric Modeling on 3D Structures, NeurIPS 2023