Calculating GDT TS: Difference between revisions

Line 42:

8. In a separate tab, get the same form [http://linum.proteinmodel.org/AS2TS/LGA/lga.html LGA = pairwise protein structure comparison].

9. ~~Enter your email address~~.

9. Make sure there are no molecules specified in sections '''1, 2, or 3''' of the form. If necessary, press the '''Clear Form''' button.

10. ~~Paste the entire output of Run 1 into box '''4'''~~.

10. Enter your email address.

11. In the parameters slot, change -4 to '''-3''', and add '''-d:4.0  -al''' at the end. So the complete parameters for Run 2 should be

11. Paste the entire output of Run 1 into box '''4'''.

12. In the parameters slot, change -4 to '''-3''', and add '''-d:4.0  -al''' at the end. So the complete parameters for Run 2 should be

:'''-3 -o2 -gdc -lga_m -stral  -d:4.0  -al'''.

12. Press the '''START''' button. The output for our example:

13. Press the '''START''' button. The output for our example:

[[Image:As2ts-5a2fA-7jx6A-run2.png|border|800px]]

13. The GDT_TS score reported by the server needs to be adjusted to reflect the similarity for the entire reference structure, namely 104 residues in our example. The final GDT_TS score for structure similarity between 5a2f_A and 7jx6_A can be estimated as follows:

14. The GDT_TS score reported by the server needs to be adjusted to reflect the similarity for the entire reference structure, namely 104 residues in our example. The final GDT_TS score for structure similarity between 5a2f_A and 7jx6_A can be estimated as follows:

:'''GDT_TS = 61.111 * 90/104 = 52.88'''

Calculating GDT TS: Difference between revisions

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@@ Line 42: / Line 42: @@
 . In a separate tab, get the same form [http://linum.proteinmodel.org/AS2TS/LGA/lga.html LGA = pairwise protein structure comparison].
-. Enter your email address.
+. Make sure there are no molecules specified in sections <span class="text-red">'''1, 2, or 3'''</span> of the form. If necessary, press the '''Clear Form''' button.
-. Paste the entire output of Run 1 into box <span class="text-red">'''4'''</span>.
+. Enter your email address.
-. In the parameters slot, change -4 to '''-3''', and add '''-d:4.0 &nbsp;-al''' at the end. So the complete parameters for Run 2 should be
+. Paste the entire output of Run 1 into box <span class="text-red">'''4'''</span>.
+. In the parameters slot, change -4 to '''-3''', and add '''-d:4.0 &nbsp;-al''' at the end. So the complete parameters for Run 2 should be
 :'''-3 -o2 -gdc -lga_m -stral &nbsp;-d:4.0 &nbsp;-al'''.
 . Press the '''START''' button. The output for our example:
 [[Image:As2ts-5a2fA-7jx6A-run2.png|border|800px]]
 . The GDT_TS score reported by the server needs to be adjusted to reflect the similarity for the entire reference structure, namely 104 residues in our example. The final GDT_TS score for structure similarity between 5a2f_A and 7jx6_A can be estimated as follows:
 :<span style="font-size:160%;">'''GDT_TS = 61.111 * 90/104 = <span class="text-red">52.88</span>'''<span>