P2Rank: Protein-ligand binding site prediction from protein structure based on machine learning.

A Consensus Docking Plugin for PyMOL

3D diverse conformers generation using rdkit

an integrated tool for molecular docking and virtual screening

Web application for protein-ligand binding sites analysis and visualization

Python snippets for PyMOL to be run in Jupyterlab via the jupyterlab-snippets-multimenus extension.

AnnapuRNA: a scoring function for predicting RNA-small molecule interactions.

A program analyzing 3D protein structures from PDB to generate 2D binding motifs

ligand-based virtual screening with consensus queries

ZDOCK predictions and PDB structures in C++ and Python

User friendly molecular dynamics simulation combining Modeller, OpenMM and Google Colab: A complete guide

NeuralMD for Protein-ligand Binding Simulation, Nature Communicaitons 2025 https://www.nature.com/articles/s41467-025-67808-z

AutoCorrelation of Pharmacophore Features

backup of silicos-it's align-it-1.0.4

AutoCorrelation of Pharmacophore Features

Chemoinformatics tool for ligand-based virtual screening

An R script that uses MACCS166 chemical fingerprint and calculates Jaccard Index/Tanimoto Coefficient for a list of Aspartate Racemase Ligands

EleKit2 computes the electrostatic complementarity between a docked ligand and its protein receptor

EleKit measures the similarity of electrostatic potentials between a small molecule and a protein.

Unofficial MCP server for PoseBusters – validate molecular poses via HTTP or Spaces using the Model Context Protocol (MCP).