role-application

A versatile workflow for the generation of receptor-based pharmacophore models for virtual screening

AutoDock Vina

Jupyter Dock is a set of Jupyter Notebooks for performing molecular docking protocols interactively, as well as visualizing, converting file formats and analyzing the results.

Code for the ProteinMPNN paper

Official repository for the Boltz biomolecular interaction models

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

fpocket is a very fast open source protein pocket detection algorithm based on Voronoi tessellation. The platform is suited for the scientific community willing to develop new scoring functions and extract pocket descriptors on a large scale level. fpocket is distributed as free open source software.

A deep learning framework for molecular docking

Deep Site and Docking Pose (DSDP) is a blind docking strategy accelerated by GPUs, developed by Gao Group. For the site prediction part, several modifications are introduced to PUResNet program. The pose sampling part is similar as AutoDock Vina combined with a number of modifications.

Official Github for "PharmacoNet: deep learning-guided pharmacophore modeling for ultra-large-scale virtual screening" (Chemical Science)

A Euclidean diffusion model for structure-based drug design.

TeachOpenCADD: a teaching platform for computer-aided drug design (CADD) using open source packages and data

This package contains deep learning models and related scripts for RoseTTAFold

Training and inference code for ShEPhERD: Diffusing shape, electrostatics, and pharmacophores for bioisosteric drug design [ICLR 2025 oral]

Codes for our paper "Programming Biomolecular Interactions with All-Atom Generative Model"

The second version of the Kraken taxonomic sequence classification system

Prediction of binding residues for metal ions, nucleic acids, and small molecules.

IF-SitePred is a method for predicting ligand-binding sites on protein structures. It first generates an embedding for each residue of the protein using the ESM-IF1 (inverse folding) model, then performs point cloud clustering to identify binding site centers.

A pocket volume analyzer for use in protein modeling.