Dear Careina,

Your message is a bit confusing... Which kind of validation are you referring to? Do you want to check the geometrical quality of the backbone and side-chain rotamers, or do you want to evaluate how likely it is that the fold proposed by homology actually represents the fold of your protein?


Best,

Joana

--
Postdoctoral Researcher
Department of Protein Evolution

Max Planck Institute for Developmental Biology
Max-Planck-Ring 5
72076 Tübingen
GERMANY

On 02.03.2018 13:09, Tristan Croll wrote:
Hi Careina,

This is a little confusing. A homology model *is* a set of coordinates (usually provided as a PDB file by most servers/packages I know of). The MolProbity site at http://molprobity.biochem.duke.edu/ allows you to upload your own PDB file, and in my experience is quite forgiving regarding format.

Hope this helps,

Tristan

On 2018-03-02 11:44, Careina Edgooms wrote:
Dear all

What programs are best used for validate homology models? I know of
molprobity but if there are no coordinates I cannot use it. Is there a
way to use such programs with homology models?

Also I wish to use pdbepisa for to charaterise dimer interface but
again for homology model this cannot be done as there is no PDB model.
Does anybody know way to use PISA software on my own model that is not
deposited in PDB?

Thank you in advance
Careina

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