SCOPe: classification of large macromolecular structures in the structural classification of proteins-extended...

Area of Science:

• Structural Biology
• Bioinformatics
• Computational Biology

Background:

• The Structural Classification of Proteins-extended (SCOPe) database provides hierarchical classification of protein domains based on structural and evolutionary relationships.
• SCOPe integrates the ASTRAL compendium, offering tools for analyzing protein sequences and structures.

Purpose of the Study:

• To update and enhance the SCOPe database with a focus on larger protein structures and novel domain characteristics.
• To incorporate new classifications for spliceosome, proteasome, and RNA polymerase I, along with previously unclassified Pfam families.

Main Methods:

• Hierarchical classification of protein domains using a combination of manual curation and automated methods.
• Focus on manual curation for large protein complexes, identifying novel non-globular folds and domain extensions.
• Regular monthly updates incorporating new data from the Protein Data Bank (PDB).

Main Results:

• SCOPe release 2.07 classifies 90,992 PDB entries, representing approximately two-thirds of all PDB entries.
• Identification of distinctive features in domains from large complexes, including novel folds and disordered N- or C-terminal extensions.
• Expanded classification of previously unaddressed Pfam families and large protein structures.

Conclusions:

• The enhanced SCOPe database provides a more comprehensive classification of protein structures, particularly for complex biological machinery.
• The detailed classification aids in understanding protein evolution, function, and structural diversity.
• Regular updates ensure SCOPe remains a valuable resource for the structural biology and bioinformatics communities.