SheeP

SheeP computes explicit descriptions of β-sheets in protein structures, producing β-sheet maps that integrate hydrogen-bonding patterns and geometrical constraints to support objective structural classification.

Key Features:

• β-Sheet Map Generation: Modifies β-sheet detection from DSSP and Stride and represents results in a tabular β-sheet map detailing sheet features.
• Holistic β-Sheet Representation: Treats entire β-sheets as holistic entities rather than focusing solely on individual β-strands.
• Integration of Hydrogen Bonds and Geometrical Constraints: Uses hydrogen-bonding patterns together with geometrical constraints to determine β-sheet presence and configuration.
• Validation on SCOP Families: Demonstrated predictive architecture accuracy on 93 well-defined all-β and α/β SCOP domain families, correctly predicting architectures in 93% of cases.

Scientific Applications:

• Protein Structure Classification: Provides objective β-sheet descriptions that support structural classification efforts.
• β-Sheet Architecture Analysis: Enables detailed analysis of β-sheet arrangements within proteins, including all-β and α/β domain families.
• Functional and Interaction Studies: Supplies explicit β-sheet topology information useful for interpreting protein function and intermolecular interactions.

Methodology:

SheeP modifies DSSP and Stride β-sheet calls, constructs a tabular β-sheet map, applies hydrogen-bonding pattern analysis and geometrical constraints to define sheet configuration, and was validated against 93 all-β and α/β SCOP domain families (93% correct architecture prediction).