FLIPPER, Fast Linear Interacting Peptides Predictor

Damiano Piovesan, Paolo Bonato, Ivan Mičetić and Silvio C.E. Tosatto

Version 2.0

Introduction

This package includes the FLIPPER predictor and the MOBI software to extract LIPs and mobile residues from PDB structures. FLIPPER is a random forest classifier, MOBI identify mobile residues in NMR ensembles by comparing the atomic position in different models of the same PDB. The package is used to generate data in the MobiDB database (https://mobidb.org)

References

MOBI

Mobi 2.0: An improved method to define intrinsic disorder, mobility and linear binding regions in protein structures \ Piovesan D, Tosatto SCE. \ (2018) Bioinformatics, 34 (1), pp. 122-123 \ https://pubmed.ncbi.nlm.nih.gov/28968795/

MOBI: A web server to define and visualize structural mobility in NMR protein ensembles \ Martin AJM, Walsh I, Tosatto SCE. \ (2010) Bioinformatics, 26 (22), art. no. btq537, pp. 2916-2917 \ https://pubmed.ncbi.nlm.nih.gov/20861031/

FLIPPER

FLIPPER: Predicting and Characterizing Linear Interacting Peptides in the Protein Data Bank \ Monzon AM, Bonato P, Necci M, Tosatto SCE, Piovesan D. \ (2021) Jounral of Molecular Biology \ https://pubmed.ncbi.nlm.nih.gov/33647288/

Requirements

• Python 3

Usage

The following command prints the help page on screen:

python3 biodb_disorder.py -h

FLIPPER can be executed by just providing the PDB input and the output file:

python3 biodb_disorder.py pdb2zps.ent.gz 2zps.mjson.gz

Configuration

Check config.ini and config_flipper.json for correct paths to models. Provide absolute paths.

Output

Output is provided in multiline JSON format, e.g. one JSON document per line. Each document corresponds to one residue.

json {"pdb_id": "1jsu", "chain_id": "A", "residue_id": "25", "dssp": "S", "rsa": 0.501, "bfactor": 84.38, "bfactor_normalized": 0.488, "lip": 0.224, "lip_status": "0", "inter_contacts": 0.909, "intra_long_contacts": 1.455, "helix": 0.0, "beta": 0.455, "coil": 0.545, "delta_rsa": 0.203, "linearity": 0.836, "length_cutoff": 1.0} {"pdb_id": "1jsu", "chain_id": "A", "residue_id": "26", "dssp": "T", "rsa": 0.502, "bfactor": 86.53, "bfactor_normalized": 0.501, "lip": 0.224, "lip_status": "0", "inter_contacts": 0.818, "intra_long_contacts": 1.545, "helix": 0.0, "beta": 0.455, "coil": 0.545, "delta_rsa": 0.205, "linearity": 0.87, "length_cutoff": 1.0} {"pdb_id": "1jsu", "chain_id": "A", "residue_id": "27", "dssp": "T", "rsa": 0.499, "bfactor": 77.87, "bfactor_normalized": 0.451, "lip": 0.171, "lip_status": "0", "inter_contacts": 0.818, "intra_long_contacts": 1.636, "helix": 0.0, "beta": 0.455, "coil": 0.545, "delta_rsa": 0.206, "linearity": 0.758, "length_cutoff": 1.0} {"pdb_id": "1jsu", "chain_id": "A", "residue_id": "28", "dssp": "-", "rsa": 0.486, "bfactor": 51.83, "bfactor_normalized": 0.3, "lip": 0.123, "lip_status": "0", "inter_contacts": 0.818, "intra_long_contacts": 1.727, "helix": 0.0, "beta": 0.455, "coil": 0.545, "delta_rsa": 0.201, "linearity": 0.727, "length_cutoff": 1.0} {"pdb_id": "1jsu", "chain_id": "A", "residue_id": "29", "dssp": "E", "rsa": 0.486, "bfactor": 24.18, "bfactor_normalized": 0.14, "lip": 0.079, "lip_status": "0", "inter_contacts": 0.636, "intra_long_contacts": 2.0, "helix": 0.0, "beta": 0.545, "coil": 0.455, "delta_rsa": 0.208, "linearity": 0.811, "length_cutoff": 1.0} {"pdb_id": "1jsu", "chain_id": "A", "residue_id": "30", "dssp": "E", "rsa": 0.479, "bfactor": 21.69, "bfactor_normalized": 0.126, "lip": 0.077, "lip_status": "0", "inter_contacts": 0.545, "intra_long_contacts": 2.182, "helix": 0.0, "beta": 0.636, "coil": 0.364, "delta_rsa": 0.207, "linearity": 0.791, "length_cutoff": 1.0} {"pdb_id": "1jsu", "chain_id": "A", "residue_id": "31", "dssp": "E", "rsa": 0.468, "bfactor": 17.82, "bfactor_normalized": 0.103, "lip": 0.054, "lip_status": "0", "inter_contacts": 0.545, "intra_long_contacts": 2.273, "helix": 0.0, "beta": 0.727, "coil": 0.273, "delta_rsa": 0.202, "linearity": 0.699, "length_cutoff": 1.0, "inter_contacts_chains": ["C"]} {"pdb_id": "1jsu", "chain_id": "A", "residue_id": "32", "dssp": "E", "rsa": 0.46, "bfactor": 15.93, "bfactor_normalized": 0.092, "lip": 0.054, "lip_status": "0", "inter_contacts": 0.545, "intra_long_contacts": 2.545, "helix": 0.0, "beta": 0.727, "coil": 0.273, "delta_rsa": 0.2, "linearity": 0.718, "length_cutoff": 1.0, "inter_contacts_chains": ["C"]} {"pdb_id": "1jsu", "chain_id": "A", "residue_id": "33", "dssp": "E", "rsa": 0.457, "bfactor": 23.09, "bfactor_normalized": 0.134, "lip": 0.072, "lip_status": "0", "inter_contacts": 0.545, "intra_long_contacts": 2.545, "helix": 0.0, "beta": 0.818, "coil": 0.182, "delta_rsa": 0.204, "linearity": 0.788, "length_cutoff": 1.0, "inter_contacts_chains": ["C"]}

Where fields are:

text pdb_id chain_id residue_id dssp rsa bfactor bfactor_normalized lip lip_status inter_contacts intra_long_contacts helix beta coil delta_rsa linearity length_cutoff