I am working with a list of gene names that I would like to sort by their structural characteristics. For example, I would like to input the list and receive an output of all names with more than 2 transmembrane domains. Does anyone know of a program capable of this task?
Jan Zaucha
The best tool for your task is probably CATH.
It won't work straight out of the box as you want: you might need to query protein IDs (you can obtain a mapping from genes) and you probably have to write scripts to parse the results but that's what CATH is for - structural classification of proteins.
http://www.cathdb.info/
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