entity-protein

AutoDock Vina

A Molecular Topography MultiToolkit designed to simplify and streamline the detection, analysis, and characterization of protein pockets, cavities, channels, and binding sites.

A dependency-free cross-platform swiss army knife for PDB files.

Reduce - tool for adding and correcting hydrogens in PDB files

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

Identification of Protein-Ligand Binding Sites using dipolar EPR data

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

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

Molsystem provides a general class for handling molecular and periodic systems

MoleculeKit: Your favorite molecule manipulation kit

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.

A comprehensive library for computational molecular biology

EquiBind: geometric deep learning for fast predictions of the 3D structure in which a small molecule binds to a protein

A pocket volume analyzer for use in protein modeling.

Predicting protein-ligand binding sites using deep convolutional neural network

An open library to work with pharmacophores.

Consensus pharmacophore for Drug Design

This package contains deep learning models and related scripts for RoseTTAFold

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