Development of an AI-Coded Protein-Dye Labeling Calculator and Protocol Generator for Research and Instruction
Type of Presentation
Poster Session
Location
University Library
Start Date
4-10-2026 11:30 AM
End Date
4-10-2026 12:45 PM
Abstract
Fluorescent labeling of proteins is a critical technique in biochemistry and biology laboratories for use in immunofluorescence, flow cytometry, and dye-based assays, yet accessible computational tools for optimizing dye conjugation remain limited. To address this gap, we developed an interactive, browser-based protein-dye labeling calculator using AI-assisted coding (Claude, Anthropic) that will run on any operating system. The calculator was constructed iteratively using large language model-assisted, natural language prompts, and is freely accessible as a web application through the Henne Lab at Governors State University. This tool allows users to adjust a comprehensive set of experimentally relevant parameters, including protein molecular weight, molar extinction coefficient, protein concentration, sample volume, and desired degree of labeling (DOL). Dye parameters include the dye-to-protein molar ratio, dye extinction coefficient, and correction factor (CF) to account for dye absorbance at 280 nm. Labeling efficiency is calculated using Beer-Lambert Law-based absorbance corrections, yielding the moles of dye per mole of protein and estimated labeling yield. Default configurations include common fluorescent dyes such as NHS-fluorescein, Alexa Fluor 488, and TRITC, with the option to input custom dyes. As an added feature, the application generates downloadable protocols and data files for use in future experiments. This tool has been successfully integrated into undergraduate/graduate biochemistry courses and research, demonstrating the utility of AI-assisted development in rapidly producing accessible laboratory scientific software.
Faculty / Staff Sponsor
Walter Henne
Development of an AI-Coded Protein-Dye Labeling Calculator and Protocol Generator for Research and Instruction
University Library
Fluorescent labeling of proteins is a critical technique in biochemistry and biology laboratories for use in immunofluorescence, flow cytometry, and dye-based assays, yet accessible computational tools for optimizing dye conjugation remain limited. To address this gap, we developed an interactive, browser-based protein-dye labeling calculator using AI-assisted coding (Claude, Anthropic) that will run on any operating system. The calculator was constructed iteratively using large language model-assisted, natural language prompts, and is freely accessible as a web application through the Henne Lab at Governors State University. This tool allows users to adjust a comprehensive set of experimentally relevant parameters, including protein molecular weight, molar extinction coefficient, protein concentration, sample volume, and desired degree of labeling (DOL). Dye parameters include the dye-to-protein molar ratio, dye extinction coefficient, and correction factor (CF) to account for dye absorbance at 280 nm. Labeling efficiency is calculated using Beer-Lambert Law-based absorbance corrections, yielding the moles of dye per mole of protein and estimated labeling yield. Default configurations include common fluorescent dyes such as NHS-fluorescein, Alexa Fluor 488, and TRITC, with the option to input custom dyes. As an added feature, the application generates downloadable protocols and data files for use in future experiments. This tool has been successfully integrated into undergraduate/graduate biochemistry courses and research, demonstrating the utility of AI-assisted development in rapidly producing accessible laboratory scientific software.