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ZBH
ZBHCenter for Bioinformatics

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SIENA

Overview

SIENA is a software pipeline enabling the fully automated construction of protein structure ensembles from the PDB. Starting with a single query structure, all binding sites with high sequence similarity are extracted from the PDB, aligned, and superimposed. SIENA also handles complicated cases, such as comparing binding sites at protein domain interfaces or within multimeric proteins.

Method

SIENA works in five consecutive steps. For details on the SIENA methodology, we refer to the corresponding publication:

  1. Candidate selection from the PDB using a sequence k-mer hashing approach
  2. Structure validation and alignment using ASCONA
  3. Filtering by user-defined structure criteria
  4. Ensemble reduction to remove highly redundant structures
  5. Superposition of the binding sites' rigid regions

Datasets

https://www.zbh.uni-hamburg.de/forschung/amd/datasets/siena-dataset.html

Software Availability

We are offering SIENA as part of our ProteinsPlus web service for searches across all PDB structures. Please visit https://proteins.plus, upload your protein, and choose SIENA.

For searches on other datasets, SIENA is freely available for non-commercial and academic users for Linux, macOS, and Windows as part of our NAOMI ChemBio Suite. Note that you can also run the alignment method ASCONA locally. To download SIENA, register at https://software.zbh.uni-hamburg.de. Non-academic users can get an evaluation license free of charge. Only minimal setup steps are required to run SIENA. All feedback (software.zbh(at)uni-hamburg.de) is highly appreciated.

References

Bietz, S.; Rarey, M. SIENA: Efficient Compilation of Selective Protein Binding Site Ensembles. J Chem Inf Model 2016, 56 (1), 248-259. DOI: https://doi.org/10.1021/acs.jcim.5b00588