Difference between revisions of "Secondary Structure Prediction"
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== PSIPRED == |
== PSIPRED == |
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| − | PSIPRED delivers many different kind of output file formats. The pictures show the pdf-output which shows the secondary structure in a graphical kind. It predicts 14 alpha-helices and 15 beta-sheets. The rest are predicted coils. |
+ | PSIPRED delivers many different kind of output file formats. The pictures show the pdf-output (Figure 1 and 2, Figure 3 is the legend) which shows the secondary structure in a graphical kind. It predicts 14 alpha-helices and 15 beta-sheets. The rest are predicted coils. |
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| − | | [[Image:Psipred1.png|thumb|center|First part of the PSIPRED output]] |
+ | | [[Image:Psipred1.png|thumb|center|Figure 1: First part of the PSIPRED output]] |
| − | | [[Image:Psipred2.png|thumb|center|Second part of the PSIPRED output]] |
+ | | [[Image:Psipred2.png|thumb|center|Figure 2: Second part of the PSIPRED output]] |
| − | | [[Image:Psipred3.png |thumb|center| Legend for the PSIPRED output ]] |
+ | | [[Image:Psipred3.png |thumb|center| Figure 3: Legend for the PSIPRED output ]] |
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|} |
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| − | Back to [[http://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/Sequence-based_predictions_HEXA |
+ | Back to [[http://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/Sequence-based_predictions_HEXA Sequence-based prediction]] |
| − | + | == Jpred3 == |
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| − | The following |
+ | The following alignment (Figure 4) shows the output of Jpred3. The secondary structure elements is marked by ourself. It predicted 14 alpha-helices and 15 beta-sheets. |
| − | [[File:jpred_pic.png|thumb|center| Jpred output with colored secondary structure elements]] |
+ | [[File:jpred_pic.png|thumb|center| Figure 4: Jpred output with colored secondary structure elements]] |
| + | |||
| − | === DSSP === |
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| + | Back to [[http://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/Sequence-based_predictions_HEXA Sequence-based prediction]] |
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| + | |||
| + | == DSSP == |
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We started DSSP on the webserver with the PDBB-id. Therefore, we get the secondary structure assignment for the whole protein and not only for the alpha-subunit. The following sequence with the according secondary structure is the output for our sequence (we extracted it from the whole). It assigned 16 alpha-helices and no beta-sheet. |
We started DSSP on the webserver with the PDBB-id. Therefore, we get the secondary structure assignment for the whole protein and not only for the alpha-subunit. The following sequence with the according secondary structure is the output for our sequence (we extracted it from the whole). It assigned 16 alpha-helices and no beta-sheet. |
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Latest revision as of 21:47, 30 August 2011
PSIPRED
PSIPRED delivers many different kind of output file formats. The pictures show the pdf-output (Figure 1 and 2, Figure 3 is the legend) which shows the secondary structure in a graphical kind. It predicts 14 alpha-helices and 15 beta-sheets. The rest are predicted coils.
Back to [Sequence-based prediction]
Jpred3
The following alignment (Figure 4) shows the output of Jpred3. The secondary structure elements is marked by ourself. It predicted 14 alpha-helices and 15 beta-sheets.
Back to [Sequence-based prediction]
DSSP
We started DSSP on the webserver with the PDBB-id. Therefore, we get the secondary structure assignment for the whole protein and not only for the alpha-subunit. The following sequence with the according secondary structure is the output for our sequence (we extracted it from the whole). It assigned 16 alpha-helices and no beta-sheet.
10 20 30 40 50
| | | | |
1 - 52 LWPWPQNFQTSDQRYVLYPNNFQFQYDVSSAAQPGCSVLDEAFQRYRDLLFG
1 - 52 T TT T TTT TT TT TT HHHHHHHHHHHHHHH
1 - 52 * ** * *
1 - 52 A AAAA AAA A AA A A AA AAA AA A A
60 70 80 90 100 110
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53 - 112 TLEKNVLVVSVVTPGCNQLPTLESVENYTLTINDDQCLLLSETVWGALRGLETFSQLVWK
53 - 112 SSSSTT TTT TT SSSSSTTT SSSSSTTHHHHHHHHHHHHHHSSS
53 - 112 * ***
53 - 112 AA AA A AAAA AAA A A A A AAA A A A AA
120 130 140 150 160 170
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113 - 172 SAEGTFFINKTEIEDFPRFPHRGLLLDTSRHYLPLSSILDTLDVMAYNKLNVFHWHLVDD
113 - 172 TT SSS SSSSS T TSSSSSSSTTTT HHHHHHHHHHHHHTT SSSSS T
113 - 172
113 - 172 AA A A A A A A AAA AA A
180 190 200 210 220 230
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173 - 232 PSFPYESFTFPELMRKGSYNPVTHIYTAQDVKEVIEYARLRGIRVLAEFDTPGHTLSWGP
173 - 232 T TT THHHHHHTT TTTT HHHHHHHHHHHHHTT SSSSS TTT TTTTT
173 - 232
173 - 232 A AAA A AA A A A A AA AA A A
240 250 260 270 280 290
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233 - 292 GIPGLLTPCYSGSEPSGTFGPVNPSLNNTYEFMSTFFLEVSSVFPDFYLHLGGDEVDFTC
233 - 292 TTTT SSSSSTTTTSSSSSSSS TT HHHHHHHHHHHHHHHHH TTSSS T THH
233 - 292
233 - 292 AA A AAAAAAAAAA AAA A A A AA A A A AAA
300 310 320 330 340 350
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293 - 352 WKSNPEIQDFMRKKGFGEDFKQLESFYIQTLLDIVSSYGKGYVVWQEVFDNKVKIQPDTI
293 - 352 HHH HHHHHHHHHHT TT THHHHHHHHHHHHHHHHTTT SSSSSHHHHHTT TT S
293 - 352 * **** *
293 - 352 AA AA AAA AAAAAAAA AA A AA A AAAA A A A AAA
360 370 380 390 400 410
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353 - 412 IQVWREDIPVNYMKELELVTKAGFRALLSAPWYLNRISYGPDWKDFYVVEPLAFEGTPEQ
353 - 412 SSS TTTTT HHHHHHHHHHTT SSSS TT TTT TT THHHHHH TT TT HHH
353 - 412 *
353 - 412 AAAAAAAAAAA A AAA A A AA A AA A AA A AAA
420 430 440 450 460 470
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413 - 472 KALVIGGEACMWGEYVDNTNLVPRLWPRAGAVAERLWSNKLTSDLTFAYERLSHFRCELL
413 - 472 HTTSSSSSSSS TTT TTTTHHHHHTTHHHHHHHHHHT TT HHHHHHHHHHHHHHHH
413 - 472 * **
413 - 472 AAA A A AAA AAAAA AA A AA
480 490
| |
473 - 492 RRGVQAQPLNVGFCEQEFEQ
473 - 492 HTT TTT TT
473 - 492
473 - 492 A A A AA A AA AA
Back to [Sequence-based Prediction]
