prot2d
Prot2d is a tool for 2D protein visualization aimed at improving the comparability of protein structures through standardized 2D visualizations. Prot2d focuses on creating highly comparable representations for same-family proteins.
Getting Started
prot2d needs python version: python= ">=3.10,<3.13"
Download prot2d via pip or poetry
- pip:
pip install prot2d
- Poetry:
poetry add prot2d
Install Foldseek
Instructions for downloading the Foldseek software can be found in Foldseek's GitHub
--> prot2d 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:
!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. This allows you to execute different prot2d's functionality on example structure and see the results without needing to set up the project locally.
Instructions in the Colab help with the first hands-on.
Documentation
Prot2d's documentation can found here:
important notes:
- input PDB files need a header to work (important for predicted structures)
- prot2d'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:
Example visualizations
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)
1 maintainer
Metadata
1 maintainer
Release files for prot2d 0.5.7
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| prot2d-0.5.7.tar.gz | 2.8 MB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| prot2d-0.5.7-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 5.6 MB
Release files / prot2d-0.5.7.tar.gz
| Download URL | prot2d-0.5.7.tar.gz |
|---|---|
| Size | 2.8 MB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
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|
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BLAKE2b-256 checksum How to use checksums |
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|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
poetry/1.6.1 CPython/3.10.0 Darwin/23.0.0
|
Release files / prot2d-0.5.7-py3-none-any.whl
| Download URL | prot2d-0.5.7-py3-none-any.whl |
|---|---|
| Size | 2.8 MB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
bc0f8858e6b2d597108b360db18ba1a9ea9d791ac37c92bd568e02a8915eb0dd
|
|
BLAKE2b-256 checksum How to use checksums |
88d76af1ae34e5bebb44f403f0994506dcd2e36506704f8d1848ddb53744ddb6
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
poetry/1.6.1 CPython/3.10.0 Darwin/23.0.0
|
