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Protein Families

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Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism. Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members. If these new proteins contain similar amino acids in key locations, protein...

Protein Families

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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

DWARF--a data warehouse system for analyzing protein families.

Markus Fischer¹, Quan K Thai, Melanie Grieb

¹Institute of Technical Biochemistry, University of Stuttgart, Allmandring 31, D-70569, Germany. mf2355@columbia.edu <mf2355@columbia.edu>

BMC Bioinformatics

|November 11, 2006

Summary

The DWARF data warehouse integrates protein sequence, structure, and function data for large protein families. This system aids in understanding complex biological systems and protein engineering by analyzing sequence-structure-function relationships.

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Area of Science:

Bioinformatics
Computational Biology
Structural Biology

Background:

Integrative bioinformatics enables novel understanding of complex biological systems by analyzing diverse biological data.
The DWARF data warehouse applies integrative bioinformatics to analyze large protein families.

Purpose of the Study:

To present the DWARF data warehouse system for analyzing large protein families.
To demonstrate DWARF's application in hosting the Lipase Engineering database.

Main Methods:

DWARF integrates protein sequence, structure, and functional annotation data using a relational data model.
Data is extracted, transformed, and loaded from public resources (ExPDB, GenBank, DSSP).
Data access is provided through search/browse interfaces and analysis tools operating on annotation, sequence, or structure.

Main Results:

The DWARF system was applied to the alpha/beta-hydrolases family, hosting the Lipase Engineering database.
Release 2.3 contains 6138 sequences and 167 protein structures across 37 superfamilies and 103 homologous families.

Conclusions:

DWARF facilitates the construction of databases for large, structurally related protein families.
The system enables evaluation of sequence-structure-function relationships and aids in predicting biochemical properties for protein engineering.