thoipapy 0.0.1

Machine-learning prediction of residues driving homotypic transmembrane interactions.

THOIPApy

The Transmembrane HOmodimer Interface Prediction Algorithm (THOIPA) is a machine learning method for the analysis of protein-protein-interactions.

THOIPA predicts TM homodimer interface residues from evolutionary sequence information alone.

THOIPA was designed to complement experimental approaches, and also energy-based modelling of TM homodimers.

What does thoipapy do?

• download protein homologues with BLAST

• extract residue properties (e.g. residue conservation and polarity)

• trains a machine learning classifier

• validates the prediction performance

• creates heatmaps of residue properties and THOIPA prediction

Installation

pip install thoipapy

Dependencies

We recommend the Anaconda python distribution, which contains all the required python modules (numpy, scipy, pandas,biopython and matplotlib). THOIPApy is currently tested for python 3.6.

Pip should automatically install the pytoxr package of Mark Teese.

THOIPApy depends on the command-line programs phobius and freecontact. Both of these are only available for Linux. THOIPApy itself has been tested on several different systems running Windows and Linux.

Development status

The code has been extensively updated and annotated for public release. However is released “as is” with some known issues, limitations and legacy code. The THOIPA standalone predictor is currently available to use. The settings file and databases used for THOIPA training are not yet released.

Usage as a standalone predictor

import thoipapy
protein_name = "ERBB3"
TMD_seq = "MALTVIAGLVVIFMMLGGTFL"
full_seq = "MVQNECRPCHENCTQGCKGPELQDCLGQTLVLIGKTHLTMALTVIAGLVVIFMMLGGTFLYWRGRRIQNKRAMRRYLERGESIEPLDPSEKANKVLA"
predictions_folder = "/path/to/your/output/folder"
blastp_executable = "blastp"
phobius_executable = "phobius"
freecontact_executable = "freecontact"
thoipapy.run_THOIPA_prediction(protein_name, TMD_seq, full_seq, predictions_folder, phobius_executable, freecontact_executable)

• Standalone prediction is currently only available on Linux.

• The operating system needs to have freecontact, phobius, and NCBI_BLAST installed.

• The biopython wrapper for NCBIblast should be installed.

• Send us an email if you have any troubles during standalone usage.

Example Output

Training the machine learning algorithm using THOIPApy

This will be implemented after publication.

import THOIPApy
settings = r"D:\data\THOIPApy_settings.xlsx"
THOIPApy.run(settings)

License

THOIPApy is free software distributed under the permissive MIT License.

Contribute

THOIPApy is not yet officially published. However, feedback regarding the installation and usage of the standalone version is appreciated. Simply email us directly, or initiate an issue in Github.

Contact

For contact details, see the relevant TU-Munich websites:

Author: Bo Zeng of the Frishman lab, TU-Munich, Weihenstephan Campus

Further coding and supervision: Mark Teese of the Langosch lab, TU-Munich, Weihenstephan Campus

Citation

Citation to be added. Full Credits: Bo Zeng, Yao Xiao, Dmitrij Frishman, Dieter Langosch, Mark Teese