Practical Guide to Homology Modeling: Difference between revisions
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Advanced search procedure: | Advanced search procedure: | ||
#Copy the FASTA format sequence for your protein, for example, from UniProt.Org. | #Copy the FASTA format sequence for your protein, for example, from [http://uniprot.org UniProt.Org]. | ||
#Note the length of your sequence. | #Note the '''length''' of your sequence. | ||
#At pdb.org, go to Advanced Search. | #At [http://pdb.org pdb.org], go to Advanced Search. | ||
#Click on “Choose a query type” and select Sequence under “Sequence Features”. | #Click on “Choose a query type” and select Sequence under “Sequence Features”. | ||
#Paste your query sequence into the large box, and 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 XXX Results”. Notice that each hit starts with a large, bold PDB ID. In the “Alignment” section of the first hit, click on “Display for All Results”. Also in the “Compound” section, click “Display for All Results”. | |||
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. | |||
== References == | == References == | ||
<references/> | <references/> | ||
