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USF Upgrades Protein Structure Software; Web-Based Interface Boosts Functionality

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The Uppsala Software Factory, housed in Gerard Kleywegt’s lab at Uppsala University’s Department of Cell and Molecular Biology in Sweden, has launched two new web servers for use with its Spasm and Dejavu protein structure recognition programs.

Kleywegt wrote the underlying software for Dejavu and Spasm several years ago, but the programs were too difficult for non-experts to use, he told BioInform.

USF post-doc Dennis Madsen wrote the Perl-CGI scripts for the servers to simplify the process. They run on a dedicated server and require only a standard web browser and a graphical molecular viewer, such as Rasmol, Chime, or SwissPDBviewer.

While the software is free to the academic community, commercial users must purchase a license from USF for in-house use. The servers are free for all users, but may be installed on local machines in cases where users may not want to submit their structure data to a public server.

The Spasm server is used for the recognition of local, user-defined spatial motifs in a large database of protein structures. Such motifs may include a set of active-site or ligand-binding residues, a looping pattern of particular interest, or other small structural pattern.

The Dejavu server recognizes whether a protein structure has a folding pattern similar to any known protein structure.

Both draw from protein databases that Kleywegt has prepared, which are derived from the Research Collaboratory for Structural Bioinformatics’ Protein Data Bank. His customized databases simplify the representation of protein structures to speed up the search process. Both programs then use a post-processing program to scrutinize the hits in more detail.

Kleywegt said that while several web-based servers exist to compare global structural patterns like Dejavu, he believes the USF offers the only web-based facility for Spasm’s local pattern recognition capabilities.

Kay Diederichs, a biologist at the University of Konstanz, agrees that Spasm is a rarity in the field. She used Spasm to identify proteins with substructures similar to a lipopolysaccharide binding motif that her research team found in the crystallographic structure of the iron transporter FhuA. "Spasm was used as the ’heart’ of a combinatorial search procedure…to query the PDB for matching substructures on structurally known proteins," she said.

Diederichs noted that Spasm was the only program suitable for the purposes of the experiment, citing the fact that it is command-line oriented and can therefore be built into larger procedures, a feature not possible with stand-alone programs with a graphical user interface.

Kleywegt said that around 30 pharmaceutical and chemical companies in the US, Europe, and Japan have acquired a Dejavu license, and approximately 10 have a Spasm license.

Kleywegt did not comment on the identity of the current licensees or the cost of a commercial license.

Future plans for Kleywegt and the USF include developing similar tools for the analysis of DNA and RNA structures.

— Bernadette Toner

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