LoopGrafter

LoopGrafter performs transplantation of loop regions between structurally related proteins to generate and evaluate chimeric proteins for the analysis and design of enzyme activity, specificity, and stability.

Key Features:

• Loop identification: Identifies loop regions in two structurally related protein inputs.
• Geometric and dynamic analysis: Computes loop geometries and assesses loop similarity and dynamics.
• Chimera construction: Enumerates all possible chimeric proteins derived from potential recombination points between the input proteins.
• 3D model generation and energetic evaluation: Constructs 3D models for each chimera and evaluates their energetics for structural viability.

Scientific Applications:

• Rational protein design: Enables transplantation of dynamic loops to modulate enzymatic properties in rational design efforts.
• Enzyme engineering: Supports generation and evaluation of chimeric enzymes to explore changes in activity, specificity, and stability.
• Biotechnology and drug development: Facilitates engineering of proteins for applications in biotechnology, pharmaceutical development, and synthetic biology.

Methodology:

Accepts two structurally related proteins as input; identifies loops and analyzes their geometries and dynamics; generates all possible chimeric combinations at potential recombination points; constructs 3D models for each chimera and performs energetic evaluations.