Web-links as a means to document annotated sequence and 3D-structure alignments in systems biology

Area of Science:

• Bioinformatics
• Computational Biology
• Structural Biology

Background:

• Biological networks are crucial for understanding life processes, with proteins as key components.
• Protein functions are often inferred from homologous proteins, requiring reliable documentation.
• Current methods for linking functional annotations and experimental data can be improved.

Purpose of the Study:

• To present a novel technique for referencing annotated sequence and 3D-structure alignments using web links.
• To facilitate the dynamic viewing of alignments and associated data in the STRAP protein viewer.
• To improve the management and review of protein functional assignments in biological network reconstruction.

Main Methods:

• Developed a web link system to encode references to public protein databases (EMBL, KEGG, GenBank, PDB, Pfam, ProDom, UniProt/Swiss-Prot).
• Implemented dynamic computation of alignment gaps within the web links.
• Enabled inclusion of site-specific annotations and 3D-rendering commands in web links.
• Integrated the method into an information management system for metabolic pathway reconstruction.

Main Results:

• Successfully created a novel technique for linking protein sequence and 3D-structure alignments via web links.
• The STRAP program dynamically displays alignments and associated data upon clicking the web link.
• Eliminated the need to manually specify retrievable sequence features like active sites.
• The system aids in documenting and reviewing protein functional assignments.

Conclusions:

• The developed web link method enhances the reliability and traceability of protein functional assignments in biological networks.
• This approach facilitates easier access to and visualization of protein alignment data for researchers.
• The alignment viewer is valuable for both computational biologists and experimentalists for documenting protein investigations.