HemeFinder is a computational tool for detecting heme binding sites based exclusively on the protein structure and the geometrical predisposition of heme binding sites. This software relies on structural and physico-chemical characteristics of heme sites, including shape, residue composition, and three geometric descriptors of the protein's backbone. HemeFinder is able to predict natural heme-binding sites and explore the potential to design new ArM based on heme.

Possible applications:

• Identification of possible heme binding sites
• Detection of heme binding pathways
• Design of new ArM based on heme

The installtion requires a conda environment with few dependencies:

> conda create -n {name} python=3.9

> conda activate {name}

> git clone https://github.com/laura-tiessler/hemefinder

> pip install hemefinder

> conda install -c anaconda -c conda-forge -c jmcmurray numpy scikit-learn psutil json

The software is run from the terminal and if defaulf parameters are used only the input PDB is needed.

• Example with PDB

  > hemefinder target_name.pdb

• Example of downloading directy from PDB server:

  > hemefinder target_name

The main parameters that can be tuned for calculations are the following:

--output: Directory where outputs should be stored.

--coordinators: List of possible coordinating residues

--mutations: List of possible mutating residues

--num_coordinants: List of possible mutating residues

Other parameters can also be tuned, but it is not recommended:

--output: Directory where outputs should be stored.

The software print de results in the terminal, but also generates two output files.

1. A json file that contains the possible heme coordinating residues and its corresponding scores, sorted by score.
2. A PDB file that contains the centroid of the coordinating probes, all the probes that make up the ellipsoid and the coordinating probes. Each result is represented by different atom types (Centroid = He, ellipsoid = Xe and coordinating probes = Ne).

Example of search for heme binding site with minimum of 2 coordinating His or Cys residues.

> cd hemefinder > hemefinder examples/1dkh_clean.pdb --coordinators ['HIS', 'CYS'] --output results_1dkh

Example of search for heme binding site and introduce a His mutation if necessary.

> hemefinder examples/1dkh_clean.pdb --mutations ['HIS'] --output results_1dkh

• Free software: BSD license

This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.

• Cookiecutter: https://github.com/audreyr/cookiecutter
• audreyr/cookiecutter-pypackage: https://github.com/audreyr/cookiecutter-pypackage