RBO Aleph

RBO Aleph: Integrated Protein Structure Prediction Platform

RBO Aleph integrates template-based modeling, protein contact prediction, and ab initio structure prediction to generate three-dimensional protein structures, including targets lacking identifiable structural templates.

Key Features:

• Residue–Residue Contact Prediction: Combines evolutionary and physicochemical information to predict intramolecular residue contacts, improving structural accuracy.
• Hybrid Modeling Strategy: Automatically selects between template-based modeling and ab initio prediction based on template availability for the target protein sequence.
• Conformational Space Exploration: Utilizes predicted contact constraints to guide conformational sampling during structure prediction.
• Model Evaluation Outputs: Generates predicted structures, residue contact maps, and backbone error estimates for structural assessment.

Scientific Applications:

• Protein Structure Determination: Predicts tertiary structures for proteins with or without homologous structural templates.
• Contact Prediction Benchmarking: Demonstrated performance in CASP11 (2014) for ab initio structure and contact prediction.

Methodology:

RBO Aleph applies a hybrid framework combining template-based modeling with ab initio folding guided by residue–residue contact predictions derived from evolutionary covariation and physicochemical features. Predicted contacts constrain conformational search to optimize three-dimensional protein structure models.