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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