Hi!

Using Prime from Schrodinger, there is the option to keep the cofactors and ligands when we build homology models.

http://platinhom.github.io/ManualHom/Schrodinger/Schrodinger_2012_docs/prime/prime_user_manual.pdf

5.3.2 Including Ligands and Cofactors

Hi Ana,

Thanks for that information. I didn't use Prime to build the homology model, I used BioSerf (part of UCL's PSI-PRED). I think I'll try Prime and see how the end model compares. 

Thanks

An interesting choice with the word "fantastic", which means: existing only in imagination; proceeding merely from imagination; fabulous, imaginary, unreal; perversely or irrationally imagined [Oxford Dictionary].

British colloquialism from where I am from. Now please, stay on topic. 

Hi Ana,

I've got a question, and I think you might have a better idea than I. When using Schrodinger to perform homology modelling the initial 34 and final 5 residues are not built into the model (they aren't covered by a template it seems). However, when I perform BioSerf or I-TASSER, I get a similar homology match the also with a complete model (including residues not meet by a template). Is this because I-TASSER and BioSerf include de-novo modelling?

Just import your model along with the xray template into a Maestro project, align them, copy/paste the heme from one protein to the other, energy-minimize the complex et voila.

Dmitri - thanks for a great answer. I almost did it that way. Instead, I performed the homology modelling within Maestro, imported the earlier protein prediction structures, aligned and then spiced the N and C terminal residues. They were the only regions of the template that were not covered. 

Dear Anthony,

Is it mandatory to use Schrodinger only? U can also do the same by other structure comparison tools. 

Thanks for your interest, Mohsin.

I've finished this piece. Once I understood the User Interface of Schrodinger, I was able to:

a) Perform a homology model using BLAST with Prime (for loops) within Schrodinger.

b) Superimpose with structure from I-TASSER over the above homology model

c) Splice the missing (de novo from I-TASSER) residues onto the above model.