Fpbase Tools

Configuration File: fpbase_tools.json Tool Type: Local Tools Count: 2

This page contains all tools defined in the fpbase_tools.json configuration file.

Available Tools

FPbase_get_protein (Type: BaseRESTTool)

Get detailed data for a fluorescent protein from FPbase by its slug/short name. Returns the prote…

FPbase_get_protein tool specification

Tool Information:

  • Name: FPbase_get_protein

  • Type: BaseRESTTool

  • Description: Get detailed data for a fluorescent protein from FPbase by its slug/short name. Returns the protein sequence, spectral properties (excitation max, emission max, extinction coefficient, quantum yield, brightness, pKa, maturation time), PDB and UniProt IDs, aggregation state, and relevant publications. FPbase is the comprehensive reference database for fluorescent proteins used in biological imaging. Examples: ‘egfp’ (Ex 488/Em 507, brightness 33.5), ‘mcherry’ (Ex 587/Em 610), ‘tdtomato’ (Ex 554/Em 581), ‘itagbfp2’ (blue), ‘mirgfp’ (infrared).

Parameters:

  • slug (string) (required) Fluorescent protein slug/short name in lowercase (e.g., ‘egfp’, ‘mcherry’, ‘tdtomato’, ‘cerulean’, ‘venus’, ‘mscarlet’, ‘mirgfp’, ‘mscarlet-i’). Common GFP variants: ‘egfp’, ‘mtaggfp2’, ‘sgfp2’. Common red: ‘mcherry’, ‘mscarlet’, ‘tdtomato’. Common blue: ‘ebfp2’, ‘mtagbfp2’. NIR: ‘mirgfp’, ‘bphp1-qd’.

Example Usage:

query = {
    "name": "FPbase_get_protein",
    "arguments": {
        "slug": "example_value"
    }
}
result = tu.run(query)

FPbase_search_by_spectrum (Type: BaseRESTTool)

Search FPbase for fluorescent proteins with specific spectral properties. Filter by excitation wa…

FPbase_search_by_spectrum tool specification

Tool Information:

  • Name: FPbase_search_by_spectrum

  • Type: BaseRESTTool

  • Description: Search FPbase for fluorescent proteins with specific spectral properties. Filter by excitation wavelength range, emission wavelength range, or name. Essential for selecting appropriate fluorescent proteins for multiplexed imaging, FRET experiments, or specific microscopy setups. FPbase contains over 1000 fluorescent proteins. Common wavelength ranges: UV/violet ~350-420nm, blue ~430-480nm, cyan ~480-500nm, green ~490-530nm, yellow ~520-570nm, orange ~550-590nm, red ~590-640nm, far-red ~640-680nm, near-infrared ~680-800nm.

Parameters:

  • name__icontains ([‘string’, ‘null’]) (optional) Search by name (case-insensitive partial match, e.g., ‘GFP’, ‘cherry’, ‘scarlet’, ‘cyan’)

  • agg_exc_max__gte ([‘integer’, ‘null’]) (optional) Minimum excitation wavelength in nm (e.g., 480 for green range)

  • agg_exc_max__lte ([‘integer’, ‘null’]) (optional) Maximum excitation wavelength in nm (e.g., 520 for green range)

  • agg_em_max__gte ([‘integer’, ‘null’]) (optional) Minimum emission wavelength in nm

  • agg_em_max__lte ([‘integer’, ‘null’]) (optional) Maximum emission wavelength in nm

  • switch_type ([‘string’, ‘null’]) (optional) Filter by photoswitching: ‘b’ (basic/constitutive), ‘ps’ (photoswitchable), ‘pa’ (photoactivatable), ‘pc’ (photoconvertible)

Example Usage:

query = {
    "name": "FPbase_search_by_spectrum",
    "arguments": {
    }
}
result = tu.run(query)