Abstract
The NIH Protein Structure Initiative centers, such as the Joint Center for Structural Genomics (JCSG), have developed highly efficient technological platforms that are capable of experimentally determining the three-dimensional structures of hundreds of proteins per year. However, the overwhelming majority of the almost 5000 protein structures determined by these centers have yet to be described in the peer-reviewed literature. In a high-throughput structural genomics environment, the process of structure determination occurs independently of any associated experimental characterization of function, which creates a challenge for the annotation and analysis of structures and the publication of these results. This challenge has been addressed by developing TOPSAN (`The Open Protein Structure Annotation Network'), which enables the generation of knowledge via collaborations among globally distributed contributors supported by automated amalgamation of available information. TOPSAN currently provides annotations for all protein structures determined by the JCSG in addition to preliminary annotations on a large number of structures from the other PSI production centers. TOPSAN-enabled collaborations have resulted in insightful structure-function analysis for many proteins and have led to numerous peer-reviewed publications, as exemplified by the articles included in this issue of Acta Crystallographica Section F.
Highlights
Our knowledge of the protein-structure universe has advanced significantly in the last decade owing in part to worldwide research efforts in high-throughput (HT) structural biology (Norvell & Berg, 2007)
In the United States, such structural genomics efforts have been spearheaded by the Protein Structure Initiative (PSI; http:// www.nigms.nih.gov/Initiatives/PSI/), which is funded by the National Institutes of Health (NIH) National Institute of General Medical Sciences (NIGMS; http://www.nigms.nih.gov/)
We developed a custom C# code built on the .NET framework to retrieve information from external resources to initialize and store The Open Protein Structure Annotation Network (TOPSAN) entries for specified proteins through an Application Programming Interface (API)
Summary
Our knowledge of the protein-structure universe has advanced significantly in the last decade owing in part to worldwide research efforts in high-throughput (HT) structural biology (Norvell & Berg, 2007). The PSI centers have overcome numerous technical challenges and pioneered the development of HT pipelines for the determination of the three-dimensional structure of proteins, leading to date to close to 5000 protein structures. More details about the specific advances and contributions of our Center, the Joint Center for Structural Genomics (JCSG), are provided in the overview for the issue (Elsliger et al, 2010). The primary mechanism of sharing the results of the structures determined by the PSI centers is via deposition of the coordinates and experimental data in the Protein Data Bank (PDB) and public websites, such as the JCSG website at http://www.jcsg.org. The PSI–Structural Genomics KnowledgeBase (SGKB; http:// kb.psi-structuralgenomics.org) provides a unified interface for the collection and collation of information from individual PSI centers and currently spearheads the effort in publicizing the achievements and successes of the PSI (Berman et al, 2009).
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