Frag r Us

Frag r Us samples alternative protein backbone conformations in loop regions to enable structure-based computational design of proteins and binding interfaces.

Key Features:

• Knowledge-based smotif database: Employs a repository of super-secondary structural motifs (smotifs) derived from existing protein structures to ground sampled conformations in empirical data.
• Loop-region targeting: Specifically targets flexible loop regions and short backbone fragments that are critical for function and molecular interactions.
• Fragment-level backbone sampling: Generates alternative backbone conformations for short fragments to explore structural diversity relevant to design and specificity tuning.
• Structural feasibility and diversity: Produces structurally feasible and diverse conformations by using empirical smotif templates as sampling templates.

Scientific Applications:

• Protein Engineering: Supports design of proteins with enhanced or novel functionalities by providing alternative backbone conformations for loop remodeling.
• Drug Design: Aids refinement of binding specificities and exploration of ligand–protein interface conformational variability.
• Structural Biology: Facilitates understanding and prediction of protein interactions by sampling feasible loop region conformations.

Methodology:

Leverages existing protein structural data to construct a repository of smotifs that serve as templates for generating new backbone conformations in loop regions, producing diverse and realistic sampled structures.