I have predicted the 3D structure of my protein using homology prediction and got a structure. I dont know how to analyse the coordination sites and motifs. Can you suggest information to analyse?
You can try 3DLigandSite.
http://www.sbg.bio.ic.ac.uk/~3dligandsite/advanced.cgi
The first thing is to look at the reliability of the "model". Does it make sense is all of the sequence modelled, if not why not and what score does it give? If you think the model is representative then there are a few things to look at. I like to map the residues which are strongly conserved, these can often cluster around the active site. many modelling programs will output a multiple sequence alignment file. Also do the other sequences/structures that your model is based on give you any clues/suggestions as to active sites possible binding partners etc.. The Dali server is also very useful for looking at proteins with a similar fold http://ekhidna.biocenter.helsinki.fi/dali/start and of course as previously mentioned 3dligand site
Use first PROCHECK to analyse the model quality. Hope you also checked Ramachandran plot!!
What is the percentage identity of the template and target protein?? Whether all the active site residues are conserved, fold is preserved, did your protein belongs to same family of the template used?? Does cysteines are conserved in pairwise sequence alignment?
Coordinae site anf motif can be checked using any visualizing software ex PyMol.
Hope this helps...
This paper might help:
Eric di Luccio and Patrice Koehl : A quality metric for homology modeling: the H-factor. BMC Bioinformatics 2011, 12:48
http://www.biomedcentral.com/1471-2105/12/48
Once, you have the 3D structure of your protein. Go to PDBsum and submit your protein. PDBsum will analyze your protein and do a good analyses i.e procheck. protein interaction and structural motifs etc.
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