BioMutation: a portable graphical user interface for mutagenesis and feature analysis in proteins, nucleic acids, and...

Area of Science:

• Structural Biology
• Computational Biology
• Biomolecular Engineering

Background:

• Protein and nucleic acid mutational studies are crucial for understanding biomolecular mechanisms.
• Current computational tools often lack user-friendly interfaces for high-throughput mutagenesis.

Purpose of the Study:

• To develop BioMutation, a graphical user interface (GUI) for automated, batch-wise mutagenesis of proteins and nucleic acids.
• To provide a flexible and accessible platform for generating mutated structures for downstream analyses.

Main Methods:

• Utilizes UCSF ChimeraX functionalities for automated mutation introduction.
• Supports user-defined and class-wise amino acid substitutions in proteins.
• Enables user-specified and combinatorial substitutions in DNA and RNA.
• Generates mutated structures in standard formats (PDB, MOL2, mmCIF).
• Includes a Google Colab-based Structure Analyzer for physicochemical feature assessment.

Main Results:

• BioMutation facilitates automated, batch-wise introduction of diverse mutations.
• Generated structures are compatible with molecular docking and dynamics simulations.
• The Structure Analyzer module allows for comparative analysis of structural changes.

Conclusions:

• BioMutation offers an efficient, user-friendly solution for in silico mutagenesis.
• The tool enhances applications in structural biology, biomolecular engineering, and drug discovery.
• Provides a flexible platform for systematic exploration of sequence-structure-function relationships.