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Interactome-Seq: A Protocol for Domainome Library Construction, Validation and Selection by Phage Display and Next Generation Sequencing

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Gene3D: Multi-domain annotations for protein sequence and comparative genome analysis.

Jonathan G Lees¹, David Lee, Romain A Studer

¹Division of Biosciences, Institute of Structural and Molecular Biology, University College London, Gower Street, London WC1E 6BT, UK, Department of Infectious Disease Epidemiology, Imperial College London, St Mary's Campus, Norfolk Place, London W2 1PG, UK and Robert Koch Institut, Research Group Bioinformatics Ng4, Nordufer 20, 13353 Berlin, Germany.

Nucleic Acids Research

|November 26, 2013

Summary

This summary is machine-generated.

Gene3D is a protein domain database that now annotates over 20 million protein sequences, significantly increasing domain coverage. Novel search algorithms and 3D homology modeling enhance comparative genomic analysis.

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Published on: July 16, 2017

Area of Science:

Structural bioinformatics
Genomics
Protein domain analysis

Background:

Protein domain structure annotations are crucial for understanding protein function and evolution.
Existing databases may have limitations in sequence coverage and domain architecture resolution.

Purpose of the Study:

To enhance the Gene3D database with expanded protein sequence annotations and improved domain coverage.
To develop novel search algorithms for comparative genomic analyses of multi-domain architectures.
To integrate 3D homology modeling capabilities for protein domains.

Main Methods:

Utilized profile Hidden Markov Models (HMMs) from CATH superfamilies for domain prediction.
Integrated domain annotations from Pfam and SUPERFAMILY databases.
Developed novel search algorithms for identifying related multi-domain architectures across genomes.
Implemented a pipeline for 3D homology modeling of protein domains.

Main Results:

Annotated over 20 million unique protein sequences, a 45% increase since the last publication.
Achieved significant increases in domain coverage for protein sequences.
Resolved domain overlaps to provide comprehensive composite multi-domain architectures.
Developed and applied 3D homology modeling to the human genome.

Conclusions:

The enhanced Gene3D database provides more comprehensive protein domain annotations and improved domain coverage.
Novel search algorithms facilitate comparative genome analyses of complex multi-domain architectures.
The integration of 3D homology modeling expands the utility of Gene3D for structural and functional genomics research.