FlatProt 0.2.0

Python package for creating simplified 2D protein visualisations. Specialised on showing differences and similaritys between proteins from the same protein family.

FlatProt

FlatProt is a tool for 2D protein visualization aimed at improving the comparability of protein structures through standardized 2D visualizations. FlatProt focuses on creating highly comparable representations for same-family proteins. In this case FlatProt was used to generate comparable representatoins for 3 3FTx structures.

Contents

• Getting Started
• First Experiences with Google Colab
• Documentation
• Data
• Example Visualizations
• Domain Annotation File Format
• Runtime for Protein Sizes
• Reference

Getting Started

FlatProt needs python version: python= ">=3.10,<3.13"

Download FlatProt via pip or poetry

• pip:

pip install FlatProt

• Poetry:

poetry add FlatProt

Install Foldseek

Instructions for downloading the Foldseek software can be found in Foldseek's GitHub

• Foldseek GitHub

--> FlatProt needs the path to the foldseek executable passed as argument to the main function to be used by the program.

Install dssp

Instructions for downloading dssp can be found here:

• dssp instructions

!The program runs on the mkdssp version 4.4.0! (some sources dont provide that (brew does!))

An example download workflow for usage can also be found in the google colab

First experiences with Google Colab

For users to get to know prot2d we've prepared a Google Colab notebook with a quick tutorial through the major functions/possibilities of prot2d. Therefore the exmample protein 1kt1 is used and visualized in different ways. This allows for basic understanding of the functionalities:

• Google Colab tutorial

Instructions in the Colab help with the first hands-on.

For direct usage of prot2d including all paramters the following Collab provides functionalitys for using prot2d withput locally downloading anything. Users can upload theri own proteins to the Collab and visualize them as wanted. The runtime of the Collab is way longer than local usage. Therefore we dont advise using it for big amounts of data:

• Google Colab usage

Documentation

FlatProt's documentation can found here:

• FlatProt documentation!

important notes:

• input PDB files need a header to work (important for predicted structures)
• FlatProt's methods can also be used via command line commands (cli)

Data

This project uses datasets that can be found on Zenodo. Additional example files can be found here aswell. You can access and download the data using the following link or DOI:

• Zenodo Data

Example visualizations

3FTx: None|Anca_10|Anolis_carolinensis

3FTx - Family Overlay

1kt1 - domain visualization (family vis)

1kt1 - full protine visualization

Domain Annotation File Format:

The domain annotation is needed in the following format to be procceced by prot2d (methods for converting chainsaw annotations are included in the package documentation)

Runtime for protein sizes

The runtimes are measured on a local lightweight device.

Reference

In the following document one can find more information on the tools methodogy, result analysis and references of the shown proteins and used software.

BachelorThesis_ConstantinCarl_Enhancing-Protein-Comparability-with-Standardized-2D-Visualization.pdf