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.

PrimaryOdors.org molecular docker.

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

Modeling Protein-Ligand Interactions with GraphConvolutional Networks for Interpretable Pharmaceutical Discovery

The aim of this project is to identify and develop novel inhibitors targeting HBV DNA Polymerase and HBx Protein through Molecular Docking to block viral replication and progression of Hepatitis B.

Repository for the Taba tool

Official Implementation of CompassDock

This repository contains Jupyter notebooks used to perform computational analysis of LAT1 (SLC7A5) cholesterol binding sites, as published in JCTC

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

Tool for directed evolution of protein receptors specifically for a ligand of interest ; implementation and fine-tuning of @zaixizhang 's PocketGen focused on maximizing binding affinity.

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

[ICML 2024] Interaction-based Retrieval-augmented Diffusion Models for Protein-specific 3D Molecule Generation

intergenic region analyzer from protein alignments to draft genomes.

Contact map analysis for biomolecules; based on MDTraj

iGEM 2022 MIT_MAHE Software Tools

11th place solution of NeurIPS 2024 - Predict New Medicines with BELKA competition on Kaggle: https://www.kaggle.com/competitions/leash-BELKA

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

[Bioinformatics 2022] Cross-Modality and Self-Supervised Protein Embedding for Compound-Protein Affinity and Contact Prediction

Uniprot metal binding site challenge