Subject: [modeller_usage] question about salt bridge
From: Anna Marabotti <>
Date: Thu, 26 Mar 2009 13:17:48 +0100
I have a question about the possibility to introduce a restraint into a model. I obtained a model of a
protein, and looking at the structure I saw that an Arg residue lies in proximity of an Asp residue, but their
charged moieties are not positioned properly to infer a ion pair interaction between them. Since from other
experimental data I strongly suspect that this ion pair is present (but I am not 100% certain), I would like
to know if I can force somehow these two residues to interact each others, without disrupting the rest of the
model. The problem is not only on the side chain, because I cannot simply rotate it or use some programs like
SCWRL or so on to change the position of the side chains: also the backbone would be affected if such an ion
pair would be present. Therefore I would like to know if I can add some "soft" restraints, for example to
"ask" MODELLER: keep the charged moieties of Arg and Asp not farther than X A only if the backbone angles are
changing not more than Y degrees to do it.
Is there a way to do it?
Many thanks and best regards
Anna Marabotti, Ph.D.
Laboratory of Bioinformatics and Computational Biology
Institute of Food Science, CNR
Via Roma 64
83100 Avellino (Italy)
Phone: +39 0825 299651
Fax: +39 0825 781585
Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm
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