Question: Database Of Structurally Derived Protein Features
2
gravatar for samesense
6.3 years ago by
samesense40
United States
samesense40 wrote:

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?

database uniprot • 1.3k views
ADD COMMENTlink modified 6.0 years ago by ddofer30 • written 6.3 years ago by samesense40
2
gravatar for ddofer
6.0 years ago by
ddofer30
Israel
ddofer30 wrote:

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).

 

ADD COMMENTlink written 6.0 years ago by ddofer30
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