interface-cli

Cryptic binding pocket discovery from conformational ensembles. Open-source, reproducible, size-robust benchmarks against fpocket, PocketMiner and CryptoBench.

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

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

Parameter/topology editor and molecular simulator

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.

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

This package contains deep learning models and related scripts for RoseTTAFold

Quantum chemistry program executor and IO standardizer (QCSchema).

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

Adds or removes hydrogen atoms to achieve the appropriate molecular protonation state for a user-specified pH range

Python3 translation of AutoDockTools

Calculation of interatomic interactions in molecular structures

Library for computing dynamic non-covalent contact networks in proteins throughout MD Simulation

Predicting protein-ligand binding sites using deep convolutional neural network

A pocket volume analyzer for use in protein modeling.

SchNetPack - Deep Neural Networks for Atomistic Systems

Code for the DISCO model: General Multimodal Protein Design Enables DNA-Encoding of Chemistry

[PNAS 2025] Code of "Manifold-Constrained Nucleus-Level Denoising Diffusion Model for Structure-Based Drug Design".

Open-source tool to generate 3D-ready small molecules for virtual screening

📐 Symmetry-corrected RMSD in Python