SAM-T08

SAM-T08 predicts three-dimensional protein structures, local backbone and burial properties, and residue-residue contacts while scoring PDB templates with calibrated E-values to support structural biology investigations.

Key Features:

• Multiple Sequence Alignments: Generates three distinct multiple sequence alignments of putative homologs using different iterated search procedures.
• Local Structural Feature Prediction: Predicts local structural features including backbone properties, burial characteristics, and secondary-structure tendencies (e.g., alpha-helices and beta-sheets).
• Residue-Residue Contact Predictions: Predicts residue-residue contacts to inform spatial interactions and structural constraints within the protein.
• Template Search Significance: Provides calibrated E-values to assess the significance of template searches within the Protein Data Bank (PDB).
• Intermediate and Final Outputs: Produces detailed intermediate results alongside final 3D structure models.

Scientific Applications:

• 3D Protein Structure Prediction: Supports generation of final 3D protein structure models from sequence information.
• Functional Domain and Evolutionary Analysis: Identifies conserved regions and functional domains via multiple sequence alignments to inform evolutionary relationships.
• Residue Interaction and Contact Mapping: Provides contact maps useful for locating potential interaction sites and defining structural constraints.
• Template-based Modeling and Template Assessment: Enables template-based modeling using PDB templates and calibrated E-values to determine template relevance.
• Drug Discovery and Structural Biology Research: Supplies structural models and contact/feature predictions to support drug discovery and other structural biology applications.

Methodology:

Generates three distinct multiple sequence alignments via different iterated search procedures, predicts local backbone and burial properties and secondary-structure propensities, predicts residue-residue contacts, and computes calibrated E-values for PDB template searches.