FPbase

FPbase aggregates curated data and analytical functionality for fluorescent proteins to support microscopy experiment design and protein-engineering workflows.

Key Features:

• Data aggregation: Aggregates amino acid sequences, accession identifiers (GenBank, UniProt), directed-evolution lineages, mutational histories, photophysical and fluorescence attributes, structural models, and primary literature references.
• Free-text excerpting: Captures context-specific information from publications outside conventional schema fields via free-text excerpts.
• Lineage exploration: Enables exploration of directed-evolution lineages and mutational trajectories.
• Multi-parameter analysis: Performs multi-parameter property analysis of photophysical and fluorescence attributes.
• Spectral overlays: Generates spectral overlays matched to experimental filters and excitation sources for spectral comparison.
• FRET calculations: Calculates FRET efficiency for donor–acceptor pairs.
• Spectra viewer: Provides customizable spectra viewers linked to microscope configurations.
• Curated collections: Maintains curated, shareable fluorescent protein collections.
• Contextual guidance: Documents environmental effects (pH, fusion context, expression level, temperature) to caution against overinterpreting tabulated values.

Scientific Applications:

• Fluorophore selection for imaging: Supports informed fluorophore selection by spectral matching and multi-parameter comparison for microscopy experiments.
• Protein engineering: Informs protein-engineering strategies through analysis of directed-evolution lineages and mutational histories.
• FRET experiment design: Facilitates FRET experimental design using FRET efficiency calculations and spectral overlap assessment.
• Data sharing and reproducibility: Enables transparent, reproducible exchange of FP data and metadata for community curation and comparison.

Methodology:

Computational and visualization methods explicitly include lineage exploration, multi-parameter property analysis, spectral overlays matched to experimental filters and excitation sources, FRET efficiency calculations, customizable spectra viewers linked to microscope configurations, and free-text excerpting from publications.