GLUE-IT and PEDEL-AA: new programmes for analyzing protein diversity in randomized libraries

Area of Science:

• Molecular Biology
• Bioinformatics
• Protein Engineering

Background:

• Randomized nucleic acid libraries are crucial for protein engineering.
• Previous tools assessed DNA-level diversity but lacked protein-level analysis.
• Site-saturation mutagenesis and error-prone PCR (epPCR) are common methods for library generation.

Purpose of the Study:

• To develop computational tools for analyzing amino acid diversity in randomized libraries.
• To provide experimental design assistance for creating libraries with desired protein outcomes.
• To update existing web server capabilities for translated library analysis.

Main Methods:

• Introduction of GLUE-Including Translation (GLUE-IT) for calculating expected amino acid completeness.
• Development of CodonCalculator and AA-Calculator for codon and amino acid analysis.
• Presentation of PEDEL-AA for calculating amino acid statistics from epPCR parameters.

Main Results:

• GLUE-IT analyzes libraries with up to six independently varied codons.
• CodonCalculator and AA-Calculator facilitate experimental design for specific amino acid targets.
• PEDEL-AA provides detailed amino acid statistics, including premature termination codon analysis for epPCR libraries.

Conclusions:

• The updated web server and new tools offer comprehensive analysis of protein-level diversity in randomized libraries.
• These tools are valuable for optimizing library design and improving the efficiency of protein engineering experiments.
• The analysis of translated libraries enhances the predictability of protein function from engineered DNA sequences.