Lessons from making the Structural Classification of Proteins (SCOP) and their implications for protein structure...

Area of Science:

• Structural biology
• Bioinformatics
• Computational biology

Background:

• The Structural Classification of Proteins (SCOP) database is a key resource for protein science.
• SCOP aids in developing tools for protein structure prediction and genome annotation.
• Its development highlighted exceptions to topological rules and complex evolutionary patterns in proteins.

Purpose of the Study:

• To review documented cases of structural variations in individual proteins.
• To examine structural variations among protein homologues.
• To emphasize the importance of understanding these variations for protein structure modeling.

Main Methods:

• Literature review of SCOP database entries.
• Analysis of documented exceptions to protein folding rules.
• Compilation of cases exhibiting alternative protein structures.

Main Results:

• Identification of numerous exceptions to established protein topological rules.
• Observation of complex evolutionary histories influencing protein structure.
• Documentation of proteins with the ability to adopt alternative conformations.

Conclusions:

• Knowledge of protein structural variations is essential for advancing protein structure modeling.
• Understanding folding peculiarities enhances the utility of protein databases like SCOP.
• These insights are critical for accurate large-scale genome annotations.