Produce a list of residue-mapped structural domain instances from Pfam ids

Workflow: Produce a list of residue-mapped structural domain instances from Pfam ids

Fetched 2024-11-26 00:32:39 GMT

Verified with cwltool version 3.1.20230201224320

Retrieve and process the PDB structures corresponding to the Pfam family ids resulting in a list of residue-mapped structural domain instances along with lost structural instances (requires Data/pdbmap downloaded from Pfam and uses SIFTS resource for UniProt to PDB residue Mapping)

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Default Values
Nested Workflows
Tools
Inputs/Outputs

This workflow is Open Source and may be reused according to the terms of: https://gitlab.inria.fr/capsid.public_codes/CroMaSt.git

Note that the tools invoked by the workflow may have separate licenses.

Inputs

ID	Type	Title
siftsdir	Directory	Directory for storing all SIFTS files
lost_merged	String	Filename for Pfam inconsistent structural instances
min_dom_size	Integer	Threshold for minimum domain length
family_idsfile	File [JSON]	File with the family IDs per iteration
resmapped_file	String	Filename for CATH inconsistent structural instances

Steps

ID	Runs	Label	Doc
add_domain_positions	add_domain_num.cwl (CommandLineTool)	Add domain position labels to residue-mapped instances	The tool adds domain position labels to each structural instance within the protein in respect with the given list.
collect_lost_instances	gather_lost_resmap.cwl (CommandLineTool)	Changes the format for core structural instances (only 1st iteration)	The tool reads the given family IDs from parameter file (.yml) and writes it to a separate file according to each iteration.
filter_pfam_structures	separate_pfam.cwl (CommandLineTool)	Filter all structural instances for given Pfam families.	The tool filter raw files from Pfam to retrieves all the available structural instances from the given Pfam families. cwl-runner --cachedir=tmp_files/ --outdir=Results/ Workflow/separate_structures.cwl yml/separate_structures.yml
resmapping_pfam_structs	7a992aa9496fb902776f96073f677656 (Workflow)	Mapping of residue numbering from UniProt to PDB

Outputs

ID	Type	Label	Doc
pfam_domain_posi_file	File [CSV]	All residue-mapped domain instances with domain labels
pfam_total_lost_structures	File [JSON]	Obsolete and inconsistent domain structural instances together