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Database Of Structurally Derived Protein Features

I have a list of a thousand residues identified on uniprot proteins. I need to gather features of these residues for a classifier. Some features require protein structures. I have a pipeline for finding appropriate structures using the protein model portal, and calculating structure based features (pka, solvent accessibility, disorder, local charge, etc) using published tools. It took a lot of work to scrape the structures and trouble shoot the published tools. I would have rather used pre computed data, but I could not find such a database.

Are you aware of a protein feature database that spans all uniprot proteins? If not, do you know why such a resource has not been built?

uniprot database
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updated by fileyfood • fileyfood • written by samesense • samesense

2 answers

I wrote a feature generation program/script a while ago in python that can do a lot of this, it's very fast and local, so just run it against the fastas of the proteins you want.

(I'm currently working on a much upgraded version).

Here's the source code.

http://www.protonet.cs.huji.ac.il/neuropid/code/index.php

http://www.protonet.cs.huji.ac.il/neuropid/code/local_SLEEK_FeatureGen+_new.py

Dan

(Used in: http://neuropid.cs.huji.ac.il/ and the articles).

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updated by Ram Ram • written by ddofer • ddofer

A few databases that have protein structural features are UniProt, the RCSB PDB, and the G2P portal

Structural features from each database:

  • UniProt: PDB SIFTS secondary structures, AlphaFold confidence
  • RCSB PDB: UniProt features, Hydropathy, Disorder, Occupancy, RSR, Buried Residues, etc
  • G2P portal: UniProt features, Hydropathy, Molar mass, Secondary Structure (AlphaFold only), pockets (AlphaFold only), ASA (AlphaFold only), Disulfide bridge/H-bonds/Vander waals/Salt bridges (PDB and AlphaFold)
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written by fileyfood • fileyfood

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