Research Object Crate for CroMaSt: A workflow for domain family curation through cross-mapping of structural instances between protein domain databases

# CroMaSt: A workflow for domain family curation through cross-mapping of structural instances between protein domain databases CroMaSt (**Cro**ss **Ma**pper of domain **St**ructural instances) is an automated iterative workflow to clarify domain definition by cross-mapping of domain structural instances between domain databases. CroMaSt (for Cross-Mapper of domain Structural instances) will classify all structural instances of a given domain type into 3 different categories (core, true and domain-like). ## Requirements 1. [Conda](https://docs.conda.io/projects/conda/en/latest/) or [Miniconda](https://docs.conda.io/en/latest/miniconda.html) 2. [Kpax](http://kpax.loria.fr/download.php) Download and install conda (or Miniconda) and Kpax by following the instructions from their official site. ## Get it running (Considering the requirements are already met) 1. Clone the repository and change the directory ``` git clone https://gitlab.inria.fr/capsid.public_codes/CroMaSt.git cd CroMaSt ``` 2. Create the conda environment for the workflow ``` conda env create --file yml/environment.yml conda activate CroMaSt ``` 3. Change the path of variables in paramter file ``` sed -i 's/\/home\/hdhondge\/CroMaSt\//\/YOUR\/PATH\/TO_CroMaSt\//g' yml/CroMaSt_input.yml ``` 4. Create the directory to store files from PDB and SIFTS (if not already) ``` mkdir PDB_files SIFTS ``` 5. Download the source input data ``` cwl-runner Tools/download_data.cwl yml/download_data.yml ``` ## Basic example ### 1. First, we will run the workflow for the KH domain with family identifiers `RRM_1` and `RRM` in Pfam and CATH, respectively. Run the workflow - ``` cwl-runner --parallel --outdir=Results/ CroMaSt.cwl yml/CroMaSt_input.yml ``` ### 2. Once the iteration is complete, check the `new_param.yml` file from the `outputdir` (Results), if there is any family identifier in either `pfam` or `cath`; run the next iteration using following command (Until there is no new families explored by workflow) - ``` cwl-runner --parallel --outdir=Results/ CroMaSt.cwl Results/new_param.yml ``` ### **Extra:** Start the workflow with multiple families from one or both databases If you would like to start the workflow with multiple families from one or both databases, then simply add a comma in between two family identifiers. ``` pfam: ['PF00076', 'PF08777'] cath: ['3.30.70.330'] ``` - **Pro Tip**: Don't forget to give different path to `--outdir` option while running the workflow multiple times or at least move the results to some other location after first run. ## Run the workflow for protein domain of your choice ### 1. You can run the workflow for the domain of your choice by simply changing the family identifers in `yml/CroMaSt_input.yml` file. Simply replace the following values of family identifiers (for pfam and cath) with the family identifiers of your choice in `yml/CroMaSt_input.yml` file. ``` pfam: ['PF00076'] cath: ['3.30.70.330'] ``` ## Data files used in current version are as follows: **Files in Data directory can be downloaded as follows**: 1. File used from Pfam database: [pdbmap.gz](http://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam33.0/pdbmap.gz) 2. File used from CATH database: [cath-domain-description-file.txt](ftp://orengoftp.biochem.ucl.ac.uk:21/cath/releases/latest-release/cath-classification-data/cath-domain-description-file.txt) 3. Obsolete entries from RCSB PDB [obsolete_PDB_entry_ids.txt](https://data.rcsb.org/rest/v1/holdings/removed/entry_ids) CATH Version - 4.3.0 (Ver_Date - 11-Sep-2019) [FTP site](ftp://orengoftp.biochem.ucl.ac.uk/cath/releases/latest-release/cath-classification-data/) Pfam Version - 33.0 (Ver_Date - 18-Mar-2020) [FTP site](http://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam33.0/) ## Reference ``` Poster - 1. Hrishikesh Dhondge, Isaure Chauvot de Beauchêne, Marie-Dominique Devignes. CroMaSt: A workflow for domain family curation through cross-mapping of structural instances between protein domain databases. 21st European Conference on Computational Biology, Sep 2022, Sitges, Spain. ⟨hal-03789541⟩ ``` ## Acknowledgements This project has received funding from the Marie Skłodowska-Curie Innovative Training Network (MSCA-ITN) RNAct supported by European Union’s Horizon 2020 research and innovation programme under granta greement No 813239.

Author

Hrishikesh Dhondge, Marie-Dominique Devignes

License

MIT

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