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

Calculation of interatomic interactions in molecular structures

Protein and nucleic acid validation service

Fast and All atom Protein-Ligand Interaction Profiler

Application to assign secondary structure to proteins

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

Interface for AutoDock, molecule parameterization

Molecule Validation and Standardization

ChEMBL database structure pipelines

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

Reduce - tool for adding and correcting hydrogens in PDB files

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

Adding hydrogens to molecular models

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

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

Python3 translation of AutoDockTools

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

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

BINANA (BINding ANAlyzer) analyzes the geometries of predicted ligand poses to identify molecular interactions that contribute to binding. It is useful because accurately characterizing these interactions allows medicinal chemists to assess whether a predicted ligand merits further study. We have also created a BINANA web-browser application.