Sequences annotated by structure: a tool to facilitate the use of structural information in sequence analysis

Area of Science:

• * Structural biology
• * Bioinformatics
• * Computational biology

Background:

• * Bridging the gap between protein sequence and structural analysis is crucial for understanding protein function.
• * Identifying distant homologues is challenging using sequence data alone.

Purpose of the Study:

• * To develop a tool for identifying new protein sequences by recognizing distant homologues using structural information.
• * To create sequence annotated by structure (SAS) files that incorporate structural data into sequence analysis.
• * To provide a web interface for structural annotation and sequence-structure alignment.

Main Methods:

• * Development of a tool that generates sequence annotated by structure (SAS) files.
• * Application of structural information derived from structural analyses to protein sequences.
• * Implementation of a World Wide Web interface for sequence submission and analysis.
• * Coloring of residues based on properties like secondary structure, interatomic contacts, and active site information.

Main Results:

• * Successful generation of SAS files integrating structural data with protein sequences.
• * A web interface enabling structural annotation and alignment against known structures.
• * Visualization of sequence properties, including secondary structure and active site information.

Conclusions:

• * The developed tool effectively aids in identifying distant protein homologues using structural information.
• * SAS files provide a novel way to annotate protein sequences with structural properties.
• * The tool enhances protein sequence analysis by integrating structural insights.