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

Source code for "DeepDTA: deep drug-target binding affinity prediction"

PLACER is graph neural network for local prediction of protein-ligand conformational ensembles.

PocketGen (Nature Machine Intelligence 24): Generating Full-Atom Ligand-Binding Protein Pockets

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

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

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]

Source code for "A universal framework for accurate and efficient geometric deep learning of molecular systems" (Nature Scientific Reports)

GPU-accelerated protein-ligand docking with automated pocket detection, exploring through multi-pocket conditioning. Official Implementation of PocketVina

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

Structural Bioinformatics Training Workshop & Hackathon 2018

All in one Structure-Based Virtual Screening workflow based on the concept of consensus docking.

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

Contact map analysis for biomolecules; based on MDTraj

DeltaVina scoring function

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

[EMNLP 2025]* FusionDTI utilises a Token-level Fusion module to effectively learn fine-grained information for Drug-Target Interaction Prediction.

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

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