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Dear All,
My question is regarding the modelling of modified protein residues
(i.e. phosphotyrosine: PTR). I know the restype.lib and Modeler
libraries contain defintions for some modified residues (e.g
selenomethionine) but will not contain them all. For cases like PTR, is
it best to define my own residue type within the Modeler libraries or is
there a simpler method?
Also, I have query as to the accepted way of dealing with the format of
modified residues in PDB files. In PDB files, modified residues are
defined within the ATOM coordinates in the correct sequence position but
labelled HETATM. I assume its ok to leave them in this format? Does
Modeler read them as actual atoms or do you need to change the
labelling? My apologies if the answer to this question is rather
obvious, I just want to make sure I'm using the accepted format for
modified residues.
Many thanks,
Karen
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Karen Crum
Discovery Informatics
Inpharmatica
60 Charlotte St
London W1T 2NU
www.inpharmatica.co.uk
email:
Direct Line: 020 7074 4636
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