SIENA
SIENA is a software pipeline for the fully automated generation of protein structure ensembles from the Protein Data Bank (PDB). Starting from a single query structure, SIENA identifies binding sites with high sequence similarity, extracts the corresponding structures, and aligns and superimposes them to create comparable protein ensembles. The pipeline also supports complex structural scenarios, including binding sites located at protein domain interfaces or within multimeric proteins.
Key benefits
Fully automated generation of protein structure ensembles
Systematic search of the PDB for sequence-similar binding sites
Automated extraction, alignment, and superposition of structures
Supports binding sites at domain interfaces and in multimeric proteins
Reduces manual effort in collecting and preparing comparable structures
Enables reproducible analysis of structural variability
Applications
Analysis of protein binding-site flexibility and conformational diversity
Generation of structure ensembles for molecular docking
Comparison of related protein–ligand complexes
Investigation of conserved and variable binding-site features
Preparation of structural datasets for drug discovery and modelling
Study of binding sites in multidomain and multimeric proteins
Intended use
SIENA is intended for structural biologists, medicinal chemists, computational chemists, and researchers in structure-based drug discovery who require curated protein structure ensembles for comparative analysis, docking, or modelling. It is particularly suited for users who want to explore binding-site variability across related structures without manually searching, aligning, and superimposing PDB entries.
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