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If what you are after are the structural co-ordinates of particular amino acids crystalized individually (i.e. considered as small molecules independently of any role in proteins), then you should find them along with other small molecules in the Cambridge Structural Database.


If you are only looking for secondary structure prediction you could try the JPred-server API. On their website they refer to a script that provides a JPred user with advanced functionality for an easy submission of hundreds of JPred jobs in a sustainable manner. […] For full details on the code, how-to, and for download please check Fabian's GitHub ...

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