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 is able to deal with complicated cases like binding sites at protein domain interfaces or within homo-multimeric proteins.

Method

SIENA works in five consecutive steps, for details on the SIENA methodology we refer to [1]:

1. Candidate selection from the PDB using a sequence k-mer hashing approach

2. Structure validation and alignment using ASCONA [2]

3. Filtering by user-defined structure criteria

4. Ensemble reduction to remove highly redundant structures

5. Superposition of the binding sites' rigid regions

Software / Webservice

SIENA is part of our ProteinsPlus web service. In this environment, SIENA is set up for searches across all PDB structures. Please visit http://proteinsplus.zbh.uni-hamburg.de, upload your protein and choose SIENA. For searches on other data sets, a SIENA stand-alone version will shortly be available. Note that you can also run the alignment method ASCONA locally. For more details see http://www.zbh.uni-hamburg.de/ascona.

Datasets

Using SIENA, we created the non-intersecting binding site ensemble data set (NBSE). The set comprises 182 ensembles with more than 9,000 aligned PDB structures in total. Moreover, alignments, ligand files in sdf format and reduced ensembles are given. The whole dataset can be downloaded from here (1.2 GB in total).

People and References

[1] Bietz, S. Rarey, M.: SIENA: Efficient Compilation of Selective Protein Binding Site Ensembles. Journal of Chemical Information and Modeling,56(1): 248-59.

[2] Bietz, S. Rarey, M.: ASCONA: Rapid Detection and Alignment of Protein Binding Site Conformations. Journal of Chemical Information and Modeling, 55(8):1747–1756.