Re: [ccp4bb] validating a homlology model
Careina, Feel free to contact me about these things without using the CCP4BB list. I am sending this to the list with as purpose that others might in the future refer people with questions about homology modelling to me. After all, although the possibility to build homology models is one of the important reasons for having structures deposited in the PDB, it is not at all related to crystallography in any way other than that both techniques try to get the most precise and accurate coordinates of (macro) molecules. Gert On 2-3-2018 12:44, 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
Re: [ccp4bb] validating a homlology model
Assuming that your homology model is that of a dimer, you could put it in a large unit cell (just add CRYST1 record). The only interface you will get from pisa will be your dimer interface. If your homology model is a monomer, then pisa will not help, of course, and you would need to predict dimerization mode first. Happy Connecting. Sent from my Sprint Samsung Galaxy S® 5 Original message From: Careina Edgooms <02531c126adf-dmarc-requ...@jiscmail.ac.uk> Date: 3/2/18 6:44 AM (GMT-05:00) To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] validating a homlology model 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 advanceCareina
Re: [ccp4bb] validating a homlology model
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
Re: [ccp4bb] validating a homlology model
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
[ccp4bb] AW: [ccp4bb] validating a homlology model
Dear Careina, If you do not have coordinates, what do you have then? A sequence alignment? In that case you can look at the %identity and %homology to see how well the known structure fits the unknown structure. If you do have coordinates in some other format generated by some modeling software, you have to convert these coordinates into pdb format. Most modeling program do have a “save as” or “export” option to generate a file in pdb format. If that fails, there are also all kind of format converting programs, but then you need to tell us the format you have right now. Best, Herman Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Careina Edgooms Gesendet: Freitag, 2. März 2018 12:44 An: CCP4BB@JISCMAIL.AC.UK Betreff: [EXTERNAL] [ccp4bb] validating a homlology model 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
Re: [ccp4bb] validating a homlology model
On 02/03/2018 11:44, Careina Edgooms wrote: 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? Answers to your questions depend on your answer to this one: What is a homology model? Along with that, we might also ask: which software (if any) might you use to create a homology model?
[ccp4bb] validating a homlology model
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 advanceCareina
