BioShell Threader

BioShell Threader performs profile-to-profile alignment (1D threading) to detect protein homology and assign structural templates to individual protein domains using sequence and secondary structure profiles.

Key Features:

• Profile-to-profile alignment (1D threading): Employs sequence profiles and secondary structure profiles to compare query sequences against structural templates.
• Multiple predictors: Integrates three independent predictors to enhance the robustness of homology detection.
• SCOP-family concordance: Evaluations report approximately an 80% probability that a query sequence belongs to the same SCOP family as the top-scoring template.

Scientific Applications:

• Structural template assignment: Assigns structural templates to protein domains to support structural modeling.
• Functional inference: Enables inference of functional properties from identified homologous structures.
• Experimental design support: Guides experimental design by identifying structural homologs for target proteins.
• Drug discovery: Facilitates drug discovery efforts by providing structural homologs for target analysis.
• Evolutionary and domain studies: Supports studies of protein domains and evolutionary biology through homology detection.

Methodology:

Generates sequence and secondary structure profiles from known protein data, performs profile-to-profile alignments (1D threading), and integrates three independent predictors.