PDBe Arpeggio

This repository contains a refactored and expanded version of the arpeggio tool, modified and maintained by the PDBe team to use as part of their weekly PDB release process.

pdbe-arpeggio is a python library, that can be used to calculate interatomic contacts in a protein based on the rules defined in CREDO. This library only supports protein structures in mmCIF format.

If you make use of pdbe-arpeggio, please cite the following article:

Harry C Jubb, Alicia P Higueruelo, Bernardo Ochoa-Montaño, Will R Pitt, David B Ascher, Tom L Blundell, Arpeggio: A Web Server for Calculating and Visualising Interatomic Interactions in Protein Structures. Journal of Molecular Biology, Volume 429, Issue 3, 2017, Pages 365-371, ISSN 0022-2836,

Disclaimer

This is a refactored version of the original arpeggio by Harry Jubb. Main changes are:

• Python 3 support
• Modular architecture to make arpeggio PIP installable.
• Support for mmCIF format to process also larger structures.
• Results in JSON format.

pdbe-arpeggio doesn't do any processing of input protein structure, other than what BioPython does by default. Alternate locations and missing density are not explicitly accounted for and may result in anomalous results. Please use with caution.

Getting Started

Web Interface

If you would like to run original version of arpeggio on a small number of individual structures, the easiest way to get started is to use the web interface.

Installation

The easiest way to set up arpeggio is using Conda. Create a conda environment and install arpeggio dependencies:

conda create -n arpeggio-env python=3.9 -c conda-forge gemmi openbabel biopython
conda activate arpeggio-env
pip install pdbe-arpeggio

Dependencies

• Open Babel >= 3.0.0
• Biopython >= 1.80
• gemmi >= 0.5.8

Running arpeggio

pdbe-arpeggio 1tqn_h.cif [options]

e.g.

pdbe-arpeggio -s /A/508/ -o out/ 1tqn_h.cif

Use pdbe-arpeggio -h for available options.

Output

All the identified interactions are written in a JSON file.

Interactions

atom-atom interactions

atom-plane interactions

plane-plane interactions

Follows nomenclature established by Chakrabarti and Bhattacharyya (2007)

group-group/plane interactions

Interacting entities

Examples

atom-atom interaction

   {
        "bgn": {
            "auth_asym_id": "A",
            "auth_atom_id": "CB",
            "auth_seq_id": 313,
            "label_comp_id": "VAL",
            "label_comp_type": "P",
            "pdbx_PDB_ins_code": " "
        },
        "contact": [
            "proximal",
            "hydrophobic"
        ],
        "distance": 4.02,
        "end": {
            "auth_asym_id": "A",
            "auth_atom_id": "CBB",
            "auth_seq_id": 508,
            "label_comp_id": "HEM",
            "label_comp_type": "B",
            "pdbx_PDB_ins_code": " "
        },
        "interacting_entities": "INTER",
        "type": "atom-atom"
    },

atom-plane interaction

    {
        "bgn": {
            "auth_asym_id": "A",
            "auth_atom_id": "O",
            "auth_seq_id": 523,
            "label_comp_id": "HOH",
            "label_comp_type": "W",
            "pdbx_PDB_ins_code": " "
        },
        "contact": [
            "DONORPI"
        ],
        "distance": 3.9,
        "end": {
            "auth_asym_id": "A",
            "auth_atom_id": "C1A,C2A,C3A,C4A,NA",
            "auth_seq_id": 508,
            "label_comp_id": "HEM",
            "label_comp_type": "B",
            "pdbx_PDB_ins_code": " "
        },
        "interacting_entities": "INTER",
        "type": "atom-plane"
    },

plane-plane interaction

{
        "bgn": {
            "auth_asym_id": "A",
            "auth_atom_id": "C1B,C2B,C3B,C4B,NB",
            "auth_seq_id": 508,
            "label_comp_id": "HEM",
            "label_comp_type": "B",
            "pdbx_PDB_ins_code": " "
        },
        "contact": [
            "FT",
            "ET"
        ],
        "distance": 4.72,
        "end": {
            "auth_asym_id": "A",
            "auth_atom_id": "CD1,CD2,CE1,CE2,CG,CZ",
            "auth_seq_id": 435,
            "label_comp_id": "PHE",
            "label_comp_type": "P",
            "pdbx_PDB_ins_code": " "
        },
        "interacting_entities": "INTER",
        "type": "plane-plane"
    },

group-group interaction

    {
        "bgn": {
            "auth_asym_id": "A",
            "auth_atom_id": "C,CA,N,O",
            "auth_seq_id": 308,
            "label_comp_id": "GLU",
            "label_comp_type": "P",
            "pdbx_PDB_ins_code": " "
        },
        "contact": [
            "AMIDEAMIDE"
        ],
        "distance": 4.29,
        "end": {
            "auth_asym_id": "A",
            "auth_atom_id": "C,CA,N,O",
            "auth_seq_id": 310,
            "label_comp_id": "THR",
            "label_comp_type": "P",
            "pdbx_PDB_ins_code": " "
        },
        "interacting_entities": "INTRA_BINDING_SITE",
        "type": "group-group"
    },