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Open Access Highly Accessed Methodology article

TOPSAN: a collaborative annotation environment for structural genomics

Dana Weekes1, S Sri Krishna1, Constantina Bakolitsa1, Ian A Wilson2, Adam Godzik134* and John Wooley13*

Author Affiliations

1 Joint Center for Structural Genomics, Bioinformatics Core, Sanford-Burnham Medical Research Institute, 10901 N. Torrey Pines Road, La Jolla, CA 92037, USA

2 Joint Center for Structural Genomics, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037, USA

3 Joint Center for Structural Genomics, Bioinformatics Core, Center for Research in Biological Systems, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA

4 Joint Center for Molecular Modeling, Sanford-Burnham Medical Research Institute, 10901 N. Torrey Pines Road, La Jolla, CA 92037, USA

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BMC Bioinformatics 2010, 11:426  doi:10.1186/1471-2105-11-426

Published: 17 August 2010

Abstract

Background

Many protein structures determined in high-throughput structural genomics centers, despite their significant novelty and importance, are available only as PDB depositions and are not accompanied by a peer-reviewed manuscript. Because of this they are not accessible by the standard tools of literature searches, remaining underutilized by the broad biological community.

Results

To address this issue we have developed TOPSAN, The Open Protein Structure Annotation Network, a web-based platform that combines the openness of the wiki model with the quality control of scientific communication. TOPSAN enables research collaborations and scientific dialogue among globally distributed participants, the results of which are reviewed by experts and eventually validated by peer review. The immediate goal of TOPSAN is to harness the combined experience, knowledge, and data from such collaborations in order to enhance the impact of the astonishing number and diversity of structures being determined by structural genomics centers and high-throughput structural biology.

Conclusions

TOPSAN combines features of automated annotation databases and formal, peer-reviewed scientific research literature, providing an ideal vehicle to bridge a gap between rapidly accumulating data from high-throughput technologies and a much slower pace for its analysis and integration with other, relevant research.