Webservice/Download Options For Homology Models

Question

[andreas.steffen]

Hi,

I am looking for a webservice from which I can programmatically download homology model(s) for a given transcript accession code of human genes. Swiss-Model seems to explicitely forbid to scrape structures from their wepage (see FAQ: http://swissmodel.expasy.org/?pid=smd06) and they don't offer an API. Is there any other webservice which would allow for this? Alternatively, is there any repository of homology models for all human genes that I could download?

Very many thanks in advance, A.

[Neilfws]

Please define "transcript accession code." You mean something like an Ensembl transcript ID?

Answer 1

[Neilfws]

is there any repository of homology models

There are at least 3:

• SWISS-MODEL Repository
• ModBase
• Protein Model Portal

[andreas.steffen]

many thanks! Problem is I need one providing an API or the possibility to download.

[Neilfws]

ModBase - probably the best of the 3 - provides FTP download: ftp://salilab.org/databases/modbase/.

Answer 2

[Fabrice Jossinet]

I just found that in the README of the ModBase FTP:

All models for a database ID:

http://salilab.org/modbase/retrieve?databaseID=database_id_from_summary_file
for example:
curl "http://salilab.org/modbase/retrieve?databaseID=Q12321"

One specific model:

http://salilab.org/modbase/retrieve?modelID=modelid_from_summary_file
for example:
curl "http://salilab.org/modbase/retrieve?modelID=064dd62ea7483831c9cfc1f72499630e"