3D pharmacophore signatures and fingerprints

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

implicit or explicit water model based docking with Autodock vina engine. supporting pharmacophore /position constrained docking

PyRod - Tracing water molecules in molecular dynamics simulations

Knowledge-Guided Diffusion Model for 3D Ligand-Pharmacophore Mapping

Generate Simple Pharmacophore Models with RDKit

PhoreGen: Pharmacophore-Oriented 3D Molecular Generation towards Efficient Feature-Customized Drug Discovery https://www.nature.com/articles/s43588-025-00850-5

Consensus pharmacophore for Drug Design

Updated version of Silicos-it's pharmacophore-based alignment tool (Align-it)

Python API for Pharmer

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

Pharmacophores Study Group

AutoCorrelation of Pharmacophore Features

Claude Plugin for CompChem , Drug Discovery & Organic Chemistry reasoning

de novo generation of synthetically feasible structures matching a 3D pharmacopohre model

Optimus Chem - Comprehensive Chemical Analysis Package

Hardware accelerator for comparing molecule fingerprints.

ZincPharmer Tutorial

Locates, scores, and predicts potential areas of ligand binding using a soft-core repulsion force over a grid.