Resource For Functional Studies Using Directed Mutagenesis

Question

[Will]

Hi all,

I'm looking for a resource that curates functional annotations associated with directed mutagenesis experiments. I'm doing an NLP project for extracting mentions of directed mutagenesis experiments, stuff like A237I, and associating them with their functional implications. So I need a collection to use for a gold-standard.

I don't really care what organism since I'm building it to be pretty general ... I just need something.

Thanks a bunch,

-Will

[Andrew Su]

... and I don't think you only mean "directed mutagenesis", since human variants can also be annotated with specific functions and are (we hope) the result of natural variation.

[Will]

I'm mostly looking for experiments which characterize molecular dyfunction of the variants ... which may have been found from natural variants but are likely to be confirmed by engineered means.

But yes, anything that mentions a protein mutation and associated dysfunction is good enough for this.

Answer 1

[Andrew Su]

Perhaps the "Allelic variants" section of OMIM (e.g., for TP53)? Some of the entries use that notation, but some don't... Might be enough to construct a gold standard though...

Better idea, use snpedia (example). You can link to the amino acid mutation through dbSNP (example), though probably still have to text mine out the functional annotations.

[Will]

I was hoping for something more along the lines of molecular function, ie. A mutation in GeneA A237I loses ability to bind to GeneB. But the disease relation is at least something.