I'd first make a large list of wanted protein names. UniProt is a good resource. It lets you filter by organism (I assumed Homo sapiens but maybe you want to include other model organisms)

On uniprot.org go directly to 'advanced' and select whatever you think pertains to your case.

It's easy to use the webform, using queries like:

taxonomy:"Homo sapiens (Human) [9606]" AND ( thrombosis OR coagulation )

(that yields ~500 records)

You can filter by any term, and/or using Keywords, GO terms, domain names, etc.

The 'Download" button then contains the url to download (as fasta, text, or whatever). You can also prescribe the columns needed (when viewing in the browser or downloading the selection as csv).

Easy to use interactively and also not hard to build these urls yourself.

Once you have limited your list of protein names in this way, you can also use them to filter down the pubmed records.

Possibly useful too: MesH and Entrez E-Utilities (there is a perl variant)

In reply to Re: Recognizing protein name by erix
in thread Recognizing protein name by pdahal

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