Protoss
Protoss is a fully automated tool for adding hydrogen atoms to protein–ligand complexes and assigning chemically plausible protonation and tautomeric states. It optimizes the hydrogen-bond network of the complex to determine suitable hydrogen coordinates for both protein and ligand molecules, supporting reliable preparation of structural models for downstream analysis.
Key benefits
Fully automated placement of missing hydrogen atoms
Assignment of plausible protonation and tautomeric states
Joint treatment of protein and ligand molecules
Optimization of the hydrogen-bond network
Fast, web-based analysis without local installation
Supports consistent preparation of protein–ligand structures
Applications
Preparation of protein–ligand complexes for molecular docking
Structure-based drug design and virtual screening
Analysis of hydrogen-bond networks
Refinement of ligand-binding site models
Preparation of structures for molecular modelling and simulation
Assessment of protonation states in experimentally determined complexes
Intended use
Protoss is intended for structural biologists, medicinal chemists, computational chemists, and researchers in structure-based drug discovery working with protein–ligand complexes. It is particularly suited for users who require automated and chemically consistent hydrogen placement and protonation-state assignment before docking, modelling, or interaction analysis.
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