Definition and classification of evaluation units for CASP10

Area of Science:

• Computational biology
• Structural biology
• Bioinformatics

Background:

• The Critical Assessment of protein Structure Prediction (CASP) experiments evaluate protein structure prediction methods.
• Protein targets in CASP are typically divided into evaluation units (EUs) for assessment.

Purpose of the Study:

• To describe the definition and classification of EUs for CASP10.
• To detail the challenges encountered and their resolutions during EU definition and classification.
• To introduce and evaluate multidomain EUs for assessing interdomain arrangements.

Main Methods:

• EUs were defined as individual structural domains or, in CASP10, as novel multidomain units.
• EUs were classified into template-based modeling (TBM) or free modeling (FM) categories.
• Classification was based on sequence and structural similarity searches for templates, with case-by-case evaluation for ambiguous cases.

Main Results:

• CASP10 introduced multidomain EUs, including three novel arrangements, to assess interdomain orientation prediction.
• The TBM category was assigned if sequence similarity searches yielded a template.
• The FM category was assigned if structural similarity searches failed to find a template.

Conclusions:

• The CASP10 methodology expanded EU definition to include multidomain structures, focusing on interdomain arrangements.
• A clear classification system for EUs into TBM and FM was established, with provisions for ambiguous cases.
• The approach facilitated a more comprehensive evaluation of protein structure prediction techniques.