PyCoM Generator

This code was written for the creation of the PyCoM database. It was written to run on the Jade2 HPC at Oxford and the Young HPC at UCL.

The resulting project/database, PyCoM, can be found on https://pycom.brunel.ac.uk.

This git repo is also of interest, as it contains the library for interacting with the database created by this: https://github.com/cemiu/pycom.

My work on this project was funded by the Department of Computer Science, Brunel University London.

DATABASE DOWNLOAD

https://pycom.brunel.ac.uk/

Info

Pipeline tools

Link to uniprot databases - http://gwdu111.gwdg.de/~compbiol/uniclust/2022_02/

Sequence alignment

• hhsuite https://github.com/soedinglab/hh-suite

Coevolution matrix

• ccmpred https://github.com/soedinglab/CCMpred

DATABASE CONTENT

- Uniprot ID
- protein name / sequence / number of residues
- organism name / taxonomy
- list of PDBs
- Enzyme classification ID
- CATH classification ID
- secondary srtucture composition
	- %Helix
	- %Beta
	- %Coil/turn
- keywords (PTMs, others; see. https://www.uniprot.org/help/keywords)
- diseases
- cofactors
- ligand/substrate