method-rule-based

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

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

Fast and All atom Protein-Ligand Interaction Profiler

Interface for AutoDock, molecule parameterization

Molecule Validation and Standardization

The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants

Protein and nucleic acid validation service

Application to assign secondary structure to proteins

Calculation of interatomic interactions in molecular structures

ChEMBL database structure pipelines

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

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

Python3 translation of AutoDockTools

PDBFixer fixes problems in PDB files

Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to 📝 Schake, Bolz, et al. (2025), https://doi.org/10.1093/nar/gkaf361

Reduce - tool for adding and correcting hydrogens in PDB files

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

A versatile workflow for the generation of receptor-based pharmacophore models for virtual screening

Adding hydrogens to molecular models

Plausibility checks for generated molecule poses.