Question: Topology of residues in proteins
1
gravatar for agonic
3.9 years ago by
agonic20
.
agonic20 wrote:

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 • 955 views
ADD COMMENTlink written 3.9 years ago by agonic20
1

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 REPLYlink written 3.9 years ago by microfuge1.6k
1

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 REPLYlink modified 3.9 years ago • written 3.9 years ago by natasha.sernova3.7k
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