method-rule-based

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

Fast and All atom Protein-Ligand Interaction Profiler

Application to assign secondary structure to proteins

Protein and nucleic acid validation service

Calculation of interatomic interactions in molecular structures

Interface for AutoDock, molecule parameterization

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

Molecule Validation and Standardization

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

Python3 translation of AutoDockTools

ChEMBL database structure pipelines

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

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

PDBFixer fixes problems in PDB files

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

Reduce - tool for adding and correcting hydrogens in PDB files

Adding hydrogens to molecular models

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

Contact map analysis for biomolecules; based on MDTraj