Dataset Information

SitesBase: a database for structure-based protein-ligand binding site comparisons.

ABSTRACT: There are many components which govern the function of a protein within a cell. Here, we focus on the molecular recognition of small molecules and the prediction of common recognition by similarity between protein-ligand binding sites. SitesBase is an easily accessible database which is simple to use and holds information about structural similarities between known ligand binding sites found in the Protein Data Bank. These similarities are presented to the wider community enabling full analysis of molecular recognition and potentially protein structure-function relationships. SitesBase is accessible at http://www.bioinformatics.leeds.ac.uk/sb.

SUBMITTER: Gold ND

PROVIDER: S-EPMC1347425 | biostudies-literature | 2006 Jan

REPOSITORIES: biostudies-literature

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SitesBase: a database for structure-based protein-ligand binding site comparisons.

Gold Nicola D ND Jackson Richard M RM

Nucleic acids research 20060101 Database issue

There are many components which govern the function of a protein within a cell. Here, we focus on the molecular recognition of small molecules and the prediction of common recognition by similarity between protein-ligand binding sites. SitesBase is an easily accessible database which is simple to use and holds information about structural similarities between known ligand binding sites found in the Protein Data Bank. These similarities are presented to the wider community enabling full analysis ...[more]

PMID: 16381853

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Project description:BackgroundA recent analysis of protein sequences deposited in the NCBI RefSeq database indicates that ~8.5 million protein sequences are encoded in prokaryotic and eukaryotic genomes, where ~30% are explicitly annotated as "hypothetical" or "uncharacterized" protein. Our Comparison of Protein Active-Site Structures (CPASS v.2) database and software compares the sequence and structural characteristics of experimentally determined ligand binding sites to infer a functional relationship in the absence of global sequence or structure similarity. CPASS is an important component of our Functional Annotation Screening Technology by NMR (FAST-NMR) protocol and has been successfully applied to aid the annotation of a number of proteins of unknown function.FindingsWe report a major upgrade to our CPASS software and database that significantly improves its broad utility. CPASS v.2 is designed with a layered architecture to increase flexibility and portability that also enables job distribution over the Open Science Grid (OSG) to increase speed. Similarly, the CPASS interface was enhanced to provide more user flexibility in submitting a CPASS query. CPASS v.2 now allows for both automatic and manual definition of ligand-binding sites and permits pair-wise, one versus all, one versus list, or list versus list comparisons. Solvent accessible surface area, ligand root-mean square difference, and Cβ distances have been incorporated into the CPASS similarity function to improve the quality of the results. The CPASS database has also been updated.ConclusionsCPASS v.2 is more than an order of magnitude faster than the original implementation, and allows for multiple simultaneous job submissions. Similarly, the CPASS database of ligand-defined binding sites has increased in size by ~ 38%, dramatically increasing the likelihood of a positive search result. The modification to the CPASS similarity function is effective in reducing CPASS similarity scores for false positives by ~30%, while leaving true positives unaffected. Importantly, receiver operating characteristics (ROC) curves demonstrate the high correlation between CPASS similarity scores and an accurate functional assignment. As indicated by distribution curves, scores ≥ 30% infer a functional similarity. Software URL: http://cpass.unl.edu.

Dataset Information

SitesBase: a database for structure-based protein-ligand binding site comparisons.

Publications

SitesBase: a database for structure-based protein-ligand binding site comparisons.

Similar Datasets

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