Raphael

Raphael detects solenoid repeats in protein structures and characterizes their periodicity and insertions from structural data.

Key Features:

• Solenoid Domain Recognition: Identifies solenoid domains within protein structures.
• Periodicity Determination: Determines solenoid periodicity with a Spearman correlation coefficient of 0.877 versus manually established periodicities.
• Insertion Assignment: Assigns insertions within identified solenoid structures with a baseline Q(2) value of 79.8%.
• Classification Accuracy: Classifies 89.5% of solenoid proteins and 97.2% of non-solenoid proteins correctly.
• Novel Repeat Discovery: Identified 1,931 highly confident repeat structures not previously annotated as solenoids in Protein Data Bank records.

Scientific Applications:

• Repeat Discovery: Discovery of previously unannotated solenoid repeats within Protein Data Bank entries.
• Evolutionary Biology: Analysis of rapid evolution and periodicity of repeat proteins in evolutionary studies.
• Molecular Dynamics: Providing structural annotations to inform molecular dynamics simulations of repeat proteins.
• Drug Design: Supporting structure-based drug design by identifying repeating structural motifs.

Methodology:

Employs a geometric approach that mimics manual classification techniques and generates numeric parameters optimized for maximum performance to enable recognition, periodicity determination, and insertion assignment.