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This article is part of the supplement: IEEE 7th International COnference on Bioinformatics and Bioengineering at Harvard Medical School

Open Access Research

The FEATURE framework for protein function annotation: modeling new functions, improving performance, and extending to novel applications

Inbal Halperin1, Dariya S Glazer1, Shirley Wu2 and Russ B Altman23*

Author Affiliations

1 Department of Genetics, 318 Campus Drive, Clark Center S240, Stanford, CA 94305, USA

2 Program in Biomedical Informatics, MSOB X-215, 251 Campus Drive, Stanford, CA 94305, USA

3 Department of Bioengineering, 318 Campus Drive, Clark Center S170, Stanford, CA 94305, USA

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BMC Genomics 2008, 9(Suppl 2):S2  doi:10.1186/1471-2164-9-S2-S2

Published: 16 September 2008

Abstract

Structural genomics efforts contribute new protein structures that often lack significant sequence and fold similarity to known proteins. Traditional sequence and structure-based methods may not be sufficient to annotate the molecular functions of these structures. Techniques that combine structural and functional modeling can be valuable for functional annotation. FEATURE is a flexible framework for modeling and recognition of functional sites in macromolecular structures. Here, we present an overview of the main components of the FEATURE framework, and describe the recent developments in its use. These include automating training sets selection to increase functional coverage, coupling FEATURE to structural diversity generating methods such as molecular dynamics simulations and loop modeling methods to improve performance, and using FEATURE in large-scale modeling and structure determination efforts.