Structure Comparison and Analysis
- CAD-score – contact area-based comparison of structures and interfaces of proteins, nucleic acids, and their complexes
- GTalign – high-performance search and alignment of macromolecular structures and complexes
- PPI3D – searching, analyzing, and modeling protein–protein, protein–peptide, and protein–nucleic acid interactions in the context of three-dimensional structures
- VoroContacts – analysis and interactive visualization of interatomic contacts in macromolecular structures
- VoroMQA – assessment of protein structure quality using interatomic contact areas
- Voronota – a software package for fast Voronoi tessellation-based analysis of three-dimensional macromolecular structures
- VoroIF-GNN – assessment of protein–protein interface accuracy in structural models using a graph neural network and Voronoi tessellation-derived features
- FTDMP – a software system for running docking experiments and scoring/ranking multimeric structural models
Sequence Search and Analysis
- COMER Web Server – sensitive protein homology searches and sequence analysis using profile–profile comparison
- COMER2 – GPU-accelerated software for sensitive and specific protein remote-homology searches
- PDEXK – a method for detecting protein families belonging to the PD-(D/E)XK nuclease superfamily (the web server is no longer supported, but its source code remains available)
- TemStaPro – protein thermostability prediction using sequence representations from protein language models