FireProt 2.0

FireProt 2.0 designs highly stable multiple-point protein mutants by integrating structural and evolutionary information for computational protein stabilization.

Key Features:

• Multiple-point mutant design: Automated design of highly stable multiple-point protein mutants.
• Structure prediction from sequence: Uses the AlphaFold database and homology modeling to obtain structural models directly from amino acid sequences.
• Combination optimization (Bron–Kerbosch): Applies the Bron–Kerbosch algorithm to construct multiple-point mutant sets while minimizing antagonistic interactions between mutations.
• Mutation modes: Supports user-specified predefined mutations and saturation mutagenesis across entire protein sequences.
• Rigidifying mutation selection: Selects rigidifying mutations based on B-factors (atomic displacement parameters) from structural data.
• Evolutionary strategies: Implements an evolution-based back-to-consensus strategy complemented by ancestral sequence reconstruction to guide stabilization.

Scientific Applications:

• Thermostability engineering: Designs thermostable protein variants by predicting and combining stabilizing mutations.
• Evolution-guided stabilization: Uses back-to-consensus and ancestral sequence reconstruction to inform stability-improving substitutions.
• Biomedical and biotechnological protein engineering: Applies to engineering proteins for biomedical and biotechnological research that require enhanced stability.

Methodology:

Integrates structural models from the AlphaFold database and homology modeling, applies the Bron–Kerbosch algorithm to construct mutant combinations minimizing antagonistic interactions, performs saturation mutagenesis or targeted mutation specification, selects rigidifying mutations based on B-factors, and employs evolution-based back-to-consensus strategy and ancestral sequence reconstruction.