Analysis of free modeling predictions by RBO aleph in CASP11

Area of Science:

• Computational Biology
• Structural Bioinformatics
• Biophysics

Background:

• The Critical Assessment of protein Structure Prediction (CASP) experiment benchmarks protein structure prediction methods.
• Automated servers play a crucial role in predicting protein structures, especially for targets lacking clear templates.

Purpose of the Study:

• To analyze the performance of the RBO Aleph server in the CASP11 free modeling category.
• To identify the key components contributing to RBO Aleph's successful ab initio protein structure prediction.

Main Methods:

• Detailed analysis of RBO Aleph's ab initio structure prediction protocol.
• Evaluation of residue-residue contact prediction using EPC-map.
• Assessment of contact-guided conformational space search via model-based search (MBS).

Main Results:

• RBO Aleph ranked as a top-performing automated server in the CASP11 free modeling category.
• The ab initio protocol, particularly EPC-map and MBS, significantly enhanced prediction quality.
• Analysis revealed potential issues in evaluating prediction methods due to complex component interactions.

Conclusions:

• RBO Aleph's success was driven by its novel ab initio prediction components.
• The interaction between components in prediction methods may complicate performance evaluation.
• Understanding these interactions is critical for advancing protein structure prediction research.