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DWARF--a Data Warehouse System for Analyzing Protein Families

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DWARF--a Data Warehouse System for Analyzing Protein Families

Markus Fischer et al. BMC Bioinformatics.

Abstract

Background: The emerging field of integrative bioinformatics provides the tools to organize and systematically analyze vast amounts of highly diverse biological data and thus allows to gain a novel understanding of complex biological systems. The data warehouse DWARF applies integrative bioinformatics approaches to the analysis of large protein families.

Description: The data warehouse system DWARF integrates data on sequence, structure, and functional annotation for protein fold families. The underlying relational data model consists of three major sections representing entities related to the protein (biochemical function, source organism, classification to homologous families and superfamilies), the protein sequence (position-specific annotation, mutant information), and the protein structure (secondary structure information, superimposed tertiary structure). Tools for extracting, transforming and loading data from public available resources (ExPDB, GenBank, DSSP) are provided to populate the database. The data can be accessed by an interface for searching and browsing, and by analysis tools that operate on annotation, sequence, or structure. We applied DWARF to the family of alpha/beta-hydrolases to host the Lipase Engineering database. Release 2.3 contains 6138 sequences and 167 experimentally determined protein structures, which are assigned to 37 superfamilies 103 homologous families.

Conclusion: DWARF has been designed for constructing databases of large structurally related protein families and for evaluating their sequence-structure-function relationships by a systematic analysis of sequence, structure and functional annotation. It has been applied to predict biochemical properties from sequence, and serves as a valuable tool for protein engineering.

Figures

Figure 1
Figure 1
Conceptual data schema for DWARF, using Logical Data Structure (LDS) notation. Each box represents an entity, which is implemented as a database table. Primary Key attributes that identify each data instance of the entity are underlined. Entities associated with the protein are shaded in dark grey on the upper left, protein structure in white on the upper right, and entities describing protein sequence properties are shaded in light grey. Lines between the entities describe existing relationships.
Figure 2
Figure 2
Distribution of protein functions for the three α/β-hydrolase classes GGGX (a), GX (b), and Y (c). Putative proteins with no function assigned and functions with a low percentage were grouped into "others".

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References

    1. Hotelier T, Renault L, Cousin X, Negre V, Marchot P, Chatonnet A. ESTHER, the database of the alpha/beta-hydrolase fold superfamily of proteins. Nucleic Acids Res. 2004;32 Database issue:D145–7. doi: 10.1093/nar/gkh141. - DOI - PMC - PubMed
    1. Giles K. Interactions underlying subunit association in cholinesterases. Protein Eng. 1997;10:677–685. doi: 10.1093/protein/10.6.677. - DOI - PubMed
    1. Barth S, Fischer M, Schmid RD, Pleiss J. Sequence and structure of epoxide hydrolases: a systematic analysis. Proteins. 2004;55:846–855. doi: 10.1002/prot.20013. - DOI - PubMed
    1. Etzold T, Ulyanov A, Argos P. SRS: Information retrieval system for molecular biology data banks. Method Enzymol. 1996;266:114–128. - PubMed
    1. McEntyre J. Linking up with Entrez. Trends Genet. 1998;14:39–40. doi: 10.1016/S0168-9525(97)01325-5. - DOI - PubMed

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