Protein three-dimensional structural databases: domains, structurally aligned homologues and superfamilies

Area of Science:

• Structural bioinformatics
• Protein domain analysis
• Computational biology

Background:

• Protein structure databases are crucial for understanding protein function and evolution.
• Identifying and aligning homologous protein structures facilitates comparative analysis.
• Databases of protein structural domains and superfamilies aid in structural classification.

Purpose of the Study:

• To report the availability of three novel web-based databases: DDBASE, HOMSTRAD, and CAMPASS.
• To provide resources for analyzing protein structural domains, homologous proteins, and superfamilies.
• To facilitate the comparison of newly determined protein structures with existing structural data.

Main Methods:

• DDBASE was generated by identifying protein structural domains using inter-secondary structural distances with the DIAL program.
• Protein alignments in superfamilies were performed using structural features and residue relationships with the COMPARER program.
• Databases provide sequence alignments in structure-annotated formats and allow visualization of superposed protein structures.

Main Results:

• DDBASE contains representative domains from homologous families, detailing domain organization and boundaries.
• HOMSTRAD and CAMPASS offer alignments of homologous proteins and superfamilies, highlighting conserved structural features.
• A graphical interface is available for viewing superposed protein structures.

Conclusions:

• The freely accessible WWW databases (DDBASE, HOMSTRAD, CAMPASS) offer valuable resources for structural bioinformatics.
• These databases enable efficient comparison of newly determined protein structures with known domains and families.
• The resources support crystallographers and researchers in structural biology for comparative studies.