NeoDesign

NeoDesign optimizes the selection of polyvalent neoantigen combinations for tumor mRNA vaccines by identifying optimal protein sequences through four integrated modules.

Key Features:

• Library Construction: Generates libraries of peptide combinations and synonymous codons for neoantigen selection.
• Optimal Path Filtering: Identifies optimal sequence paths to minimize linker usage and simplify structure.
• Linker Addition: Adds linkers between neoantigens while minimizing total linker usage.
• λ-Evaluation: Evaluates sequences to avoid unexpected neoantigens and functional domains.
• mRNA Design Preference Scheme: Balances mRNA stability and protein expression when designing mRNA sequences for the optimal protein sequence.

Scientific Applications:

• Tumor Polyvalent Neoantigen mRNA Vaccine Design: Enhances immunogenicity and safety of tumor mRNA vaccines through computational sequence optimization.
• Immunotherapy Advancement: Improves sequence design to advance tumor polyvalent neoantigen mRNA vaccine-based immunotherapy strategies.

Methodology:

NeoDesign comprises four modules: Library Construction, Optimal Path Filtering, Linker Addition, and λ-Evaluation.