Protein Pka Tools#

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

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

Available Tools#

PROPKA_compare_partner_pka (Type: ProteinPKATool)#

Compare protein pKa in a complex with the same-coordinate free partner using local PROPKA. Explic…

PROPKA_compare_partner_pka tool specification

Tool Information:

  • Name: PROPKA_compare_partner_pka

  • Type: ProteinPKATool

  • Description: Compare protein pKa in a complex with the same-coordinate free partner using local PROPKA. Explicitly retain associated chains (e.g. glycan/cofactor chains) with free_keep_chains; default extracts only partner_chain. No automatic molecular inference, affinity or pH validation. Rejects gross observed intraresidue backbone bond defects before prediction; this is not full structure validation.

Parameters:

  • pdb_id ([‘string’, ‘null’]) (optional) Four-character RCSB PDB ID to download publicly. Provide exactly one source.

  • pdb_path ([‘string’, ‘null’]) (optional) Local complex PDB file path; no upload. Provide exactly one source.

  • pdb_content ([‘string’, ‘null’]) (optional) Inline complex PDB text; no upload. Provide exactly one source.

  • partner_chain (string) (required) PDB chain character to extract unchanged; use a space for a blank chain.

  • ph_values ([‘array’, ‘null’]) (optional) pH values for independent-site fractions; defaults to [6.5, 7.4].

  • timeout_seconds ([‘integer’, ‘null’]) (optional) Bounded runtime for both calculations; defaults to 180 seconds.

  • free_keep_chains ([‘array’, ‘null’]) (optional) Additional chains belonging to the free partner, e.g. covalent glycans/cofactors. Must exist in input; omit or null to extract only partner_chain. Do not repeat partner_chain. No automatic bond or molecule inference.

Example Usage:

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

PROPKA_predict_pka (Type: ProteinPKATool)#

Predict protein pKa locally from one PDB model using optional PROPKA. Returns numbered groups, wa…

PROPKA_predict_pka tool specification

Tool Information:

  • Name: PROPKA_predict_pka

  • Type: ProteinPKATool

  • Description: Predict protein pKa locally from one PDB model using optional PROPKA. Returns numbered groups, warnings and independent-site protonated fractions. Accept a PDB ID, path or text; e.g. 1UBQ. Predictions do not validate pH-dependent binding. Rejects gross observed intraresidue backbone bond defects before prediction; this is not full structure validation.

Parameters:

  • pdb_id ([‘string’, ‘null’]) (optional) Four-character RCSB PDB ID to download publicly. Provide exactly one source.

  • pdb_path ([‘string’, ‘null’]) (optional) Local PDB file path; no upload. Provide exactly one source.

  • pdb_content ([‘string’, ‘null’]) (optional) Inline PDB text; no upload. Provide exactly one source.

  • ph_values ([‘array’, ‘null’]) (optional) pH values for independent-site fractions; defaults to [6.5, 7.4].

  • timeout_seconds ([‘integer’, ‘null’]) (optional) Bounded local worker runtime; defaults to 180 seconds.

Example Usage:

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