Topology of residues in proteins
0
1
Entering edit mode
4.7 years ago
agonic ▴ 20

I have a large dataset of Uniprot-Accessions for proteins. If I look at a specific position in these protein's sequences, I want to know if this residue is buried or exposed (i.e. on the surface). These positions represent dbSNP entries that cause missense mutations, if that is of any help. The goal is to combine that with Pfam domain data to predict whether a residue is part of a protein-protein interaction interface.

I know that I could download the PDB files, run DSSP and calculate the relative surface area, but before implementing that I wanted to make sure there isn't any database with entries like this that I have missed.

SNP sequence • 1.1k views
ADD COMMENT
1
Entering edit mode

There are several tools for predicting solvent accessibility using primary sequence. Example http://link.springer.com/chapter/10.1007%2F978-3-642-23208-4_13

ADD REPLY
1
Entering edit mode

There are other tools to compare, See these posts:

how find relative solvent accesibility

Any tools for predicting protein solvent exposure/accessibility?

This article may help too:

Predicting Protein Structural Features With Artificial Neural Networks

https://www.aaai.org/Papers/Hunter/04-Holbrook.pdf

ADD REPLY

Login before adding your answer.

Traffic: 1705 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6