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.

Methods for the parallel and distributed analysis and mining of the Protein Data Bank using MMTF and Apache Spark.

RxDock is a fork of rDock. Note: the latest code is under development. Please do git checkout patched-rdock after clone if you want patched rDock. [IMPORTANT NOTE: pull requests should be posted on GitLab, this is a read-only source code mirror]

Structural Bioinformatics Training Workshop & Hackathon 2018

Implementation of ICLR23 paper "Molecule Generation for Target Protein Binding with Structural Motifs"

Implementation of Nvidia's NeuralPlexer, for end-to-end differentiable design of functional small-molecules and ligand-binding proteins, in Pytorch

Code for our Nature Scientific Reports paper "A universal framework for accurate and efficient geometric deep learning of molecular systems"

DeltaVina scoring function

Implementation of PocketGen: Generating Full-Atom Ligand-Binding Protein Pockets

Protein target prediction using random forests and reliability-density neighbourhood analysis

Contact map analysis for biomolecules; based on MDTraj

Comparison of active site and full kinase sequences for drug-target affinity prediction and molecular generation. Full paper: https://pubs.acs.org/doi/10.1021/acs.jcim.1c00889

Methods for mapping genomic data onto 3D protein structure.

This repository contains the code for the work on protein-ligand interaction with GNNs and XAI

Methods for the parallel and distributed analysis and mining of the Protein Data Bank using MMTF and Apache Spark.

Open source code for DyScore

PSICHIC (pronounced Psychic) - PhySIcoCHemICal graph neural network for learning protein-ligand interaction fingerprints from sequence data

Flexible Artificial Intelligence Docking