entity-complex

Predict protein-ligand and catalytic pockets and perform molecular docking of a specific ligand to each predicted pocket.

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

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.

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

pythonic interface to virtual screening software

A comprehensive macromolecular library

AutoDock Vina

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

Predicting protein-ligand binding sites using deep convolutional neural network

Comprehensive library for fast, GPU accelerated molecular gridding for deep learning workflows

Open source code for AlphaFold 2.

Protein Ligand INteraction Dataset and Evaluation Resource

Identification of Protein-Ligand Binding Sites using dipolar EPR data

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

📐 Symmetry-corrected RMSD in Python

A Euclidean diffusion model for structure-based drug design.

MD pharmacophores and virtual screening

Interface for AutoDock, molecule parameterization

Open-source foundation of the user-sponsored PyMOL molecular visualization system.

Experiments with expanded ensembles to explore chemical space