Practical Guide to Homology Modeling: Difference between revisions

<table style="background:#ffff80;"><tr><td>Many assertions in this article are lacking literature citations. Help improving documentation in this article will be appreciated. Wikipedia's article on [http://en.wikipedia.org/wiki/Homology_modeling Homology modeling] is well documented, although more technical and less of a practical guide than the present article.</td></tr></table>

All published, empirically-determined, atomic-resolution, macromolecular 3D structures are available in the [[Protein Data Bank]] (PDB, pdb.org).

Here are two methods for finding out if your query amino acid sequence, or parts of it, have empirically-determined 3D structures in the PDB.

#Click on “Choose a query type” and select Sequence under “Sequence Features”.

#Paste your query sequence into the large box.

#<font color="red">Set <i>Mask low complexity</i> to No.</font>

#Click the “Submit Query” button at the lower right of the search interface box.

#The best hits will be listed first, starting below “Showing 1-25 of NNN”.  Notice that each hit starts with a large, bold PDB ID.

For each hit, notice the “Identities” above the sequence alignment box. The denominator tells you the length of the sequence alignment. The percentage tells you the sequence identity of the alignment.

For example, “Identities: 355/1045 (34%)” means that 1,045 residues of your query sequence align to the hit with 34% sequence identity (355 identical residues in the alignment). Knowing that my query had length 1,170 residues, I can see that this potential template for a homology model would enable me to model 1,045/1,170 = 89% of my query sequence. Quite often the alignment would span a much smaller portion of the full-length sequence.

<font color='red'>'''BEWARE!''' If you forgot to set <i>Mask Low Complexity</i> to NO:</font> The sequence identity percentage may be '''underestimated''' at pdb.org. This happens when pdb.org deems segments of the query sequence to be of low complexity. Such segments are marked with X’s in the sequence alignment, and excluded from the calculation of sequence identity. For example, for Saccharomyces gal4 (UniProt P04386), for the top hit (3coq), pdb.org reports “Identities: 71/89 (80%)”, while in fact the sequence identity is 100%. Note this in the sequence alignment at pdb.org:

The 18 residues marked X were not included in the identity calculation. In contrast, when the same sequence search is performed at [http://www.ebi.ac.uk/pdbe PDB-Europe], 100% sequence identity is reported. However, other aspects of the report at PDB-Europe are less satisfactory (e.g. the length of the alignment is not stated; the sequences are not numbered) and hence we recommend using pdb.org despite its misleading sequence identity percentages.

==== MobiDB via UniProt ====

At UniProt.Org, find your protein, then click on “Structure”. At the bottom of this section is usually a link to MobiDB’s report for the query protein. There, in the section ''Detailed Disorder Annotations'' are graphics showing experimental evidence for disorder (if available) and, under the heading ''Predictors'', results from several servers designed to predict intrinsic disorder.

The ''Examples'' above have links to MobiDB.

The [http://bip.weizmann.ac.il/fldbin/findex FoldIndex server] is a useful adjunct to the MobiDB report, since it is not included in that report.

===Pre-Calculated Models===

Under the subheading ''3D Structure Databases'', click on the linked UniProt ID at ProteinModelPortal. Here you will find bar graphics showing the coverage by pre-calculated homology models. Touching the blue bars reports the sequence range for each model.

 

 

Notice the section at the bottom of the page ''Remodel this protein''. This is a good option if you don't find a satisfactory model.

This give you similar coverage graphics, but limited to models generated by Swiss Model. Clicking on any one blue graphic bar shows details below, including links to download the model.

*Go to [http://swissmodel.expasy.org SwissModel.expasy.org].