Calculating GDT TS: Difference between revisions
From Proteopedia
Jump to navigationJump to search
Eric Martz (talk | contribs) |
Eric Martz (talk | contribs) |
||
| Line 21: | Line 21: | ||
4. Provide the two structures to be compared using method <span class="text-red">1, 2, or 3</span>. Specify the predicted or query structure '''first''' -- this will be superposed on the reference structure. Specify the reference structure '''second'''. | 4. Provide the two structures to be compared using method <span class="text-red">1, 2, or 3</span>. Specify the predicted or query structure '''first''' -- this will be superposed on the reference structure. Specify the reference structure '''second'''. | ||
:For a concrete example, we'll use SARS-CoV-2 ORF8, which was a target in [https://predictioncenter.org/casp14/index.cgi CASP 14]. There are two X-ray structures, [[7jtl]] and [[7jx6]]. Chain A of the latter has the highest resolution and fewest missing residues. When it was submitted (February, 2021) to the [http://ekhidna2.biocenter.helsinki.fi/dali/ DALI Server] in ''PDB 25'' mode, the top hit for structural similarity was the N-terminal domain of [[5a2f]]. So in slot <span class="text-red">1</span> | :For a concrete example, we'll use SARS-CoV-2 ORF8, which was a target in [https://predictioncenter.org/casp14/index.cgi CASP 14]. There are two X-ray structures, [[7jtl]] and [[7jx6]]. Chain A of the latter has the highest resolution and fewest missing residues. When it was submitted (February, 2021) to the [http://ekhidna2.biocenter.helsinki.fi/dali/ DALI Server] in ''PDB 25'' mode, the top hit for structural similarity was the N-terminal domain of [[5a2f]]. So in slot <span class="text-red">'''1'''</span> was entered '''5a2f_A 7jx6_A'''. | ||
5. Caveat: If you let your browser auto-fill the email address slot, make sure to clear any other slots that got auto-filled inadvertently. Otherwise you may get an error message. | 5. Caveat: If you let your browser auto-fill the email address slot, make sure to clear any other slots that got auto-filled inadvertently. Otherwise you may get an error message. | ||
