Abstract
Summary: MODexplorer is an integrated tool aimed at exploring the sequence, structural and functional diversity in protein families useful in homology modeling and in analyzing protein families in general. It takes as input either the sequence or the structure of a protein and provides alignments with its homologs along with a variety of structural and functional annotations through an interactive interface. The annotations include sequence conservation, similarity scores, ligand-, DNA- and RNA-binding sites, secondary structure, disorder, crystallographic structure resolution and quality scores of models implied by the alignments to the homologs of known structure.MODexplorer can be used to analyze sequence and structural conservation among the structures of similar proteins, to find structures of homologs solved in different conformational state or with different ligands and to transfer functional annotations. Furthermore, if the structure of the query is not known, MODexplorer can be used to select the modeling templates taking all this information into account and to build a comparative model.Availability and implementation: Freely available on the web at http://modorama.biocomputing.it/modexplorer. Website implemented in HTML and JavaScript with all major browsers supported.Contact: anna.tramontano@uniroma1.itSupplementary information: Supplementary data are available at Bioinformatics online
Highlights
Exploring the sequence, structure and function relationships between a protein and its homologs is a powerful strategy to transfer functional annotations such as, for example, ligand-binding sites and/or to detect the existence of alternative conformational states
The information contained in remote relationships may be missed or exploited only through tedious procedures
If the structure of the query protein is not known, it permits to select a template for homology modeling and to automatically build the model
Summary
Structure and function relationships between a protein and its homologs is a powerful strategy to transfer functional annotations such as, for example, ligand-binding sites and/or to detect the existence of alternative conformational states. A platform for the in-depth integrated analysis of the sequence, structure and function relationships is still missing. We describe MODexplorer, a web server that integrates sequence analysis and structure comparison with functional annotations. It provides a more complete and detailed view of the sequence, structural and functional diversity within and between protein families than existing tools. If the structure of the query protein is not known, it permits to select a template for homology modeling and to automatically build the model
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