Harmony AI: State of the Art Natural Language Processing for Genetic Engineering
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Principal Investigator: David Gaddes Organization: CFD RESEARCH CORPORATION Fiscal Year: 2023 Award: $343,491 Funding agency: National Institute of General Medical Sciences Project Summary/Abstract: Computational techniques for gene engineering, such as codon optimization, use synonymous codon changes to increase protein production. Applications for these computational gene optimizations include recombinant protein drugs, nucleic acid therapies, and mRNA vaccines. Although codon optimization increases protein production in certain systems, synonymous changes to a gene sequence can cause unexpected detrimental results to the protein. Further, researchers have been critical of codon optimization for human therapeutics as the optimization process can affect protein conformation and function, and reduce efficacy. Therefore, codon optimization may not provide an optimal strategy for increasing protein production or designing safe and effective therapeutics. CFDRC has utilized state-of-the-art natural language processing techniques to learn how synonymous codons are used by a target organism and apply this learning to gene engineering. We demonstrated our model could predict the E. Coli synonymous codon usage with 73% accuracy, significantly above prior reports. We believe that using this AI-based approach to gene engineering will provide an optimal strategy for increasing protein production and may increase the efficacy of therapeutics. Terms: <AI based platform><AI platform><AI system><Affect><Amino Acid Sequence><Artificial Intelligence><Artificial Intelligence platform><Benchmarking><Best Practice Analysis><Body Tissues><Cell Body><Cells><Chaperone><Code><Coding System><Codon><Codon Nucleotides><Complex><Computational Technique><Computer Reasoning><Computer software><DNA Sequence><DNA Therapy><Dependence><Development><Drugs><E coli><E coli Proteins><E. coli><E. coli Proteins><Engineered Gene><Ensure><Escherichia coli><Escherichia coli Proteins><Frequencies><Gene Transfer Clinical><Genes><Genetic Engineering><Genetic Engineering Biotechnology><Genetic Engineering Molecular Biology><Genetic Intervention><Human><In Vitro><Industry><Investigators><Learning><Literature><Machine Intelligence><Macromolecular Protein Complexes><Medication><Methods><Modeling><Modern Man><Molecular Chaperones><Multiprotein Complexes><Natural Language Processing><Organism><Output><Pharmaceutic Preparations><Pharmaceutical Preparations><Position><Positioning Attribute><Primary Protein Structure><Production><Protein Conformation><Proteins><RNA vaccine><RNA-based vaccine><Recombinant DNA Technology><Recombinant Proteins><Reporting><Research><Research Personnel><Researchers><Running><Software><System><Techniques><Technology><Testing><Therapeutic><Tissues><Traction><Training><Translating><Treatment Efficacy><Work><applied learning><benchmark><design><designing><developmental><drug/agent><gene repair therapy><gene therapy><gene-based therapy><genetic therapy><genetically engineered><genomic therapy><hands-on learning><human model><improved><interactive engagement><interactive learning><intervention efficacy><living system><mRNA vaccine><mRNA-based vaccine><manufacture><model of human><multi-modality><multimodality><natural language understanding><nucleic acid therapy><nucleic acid-based therapeutics><prevent><preventing><process optimization><protein expression><protein folding><protein function><protein sequence><therapeutic efficacy><therapeutic nucleic acids><therapeutically effective><therapy efficacy><tool>