Difference between revisions of "Secondary Structure Prediction"
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(Created page with "=== PSIPRED === 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 predict…") |
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| − | + | == 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 Sequence-based prediction]] |
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| − | === Jpred3 === |
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| + | == Jpred3 == |
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| − | The following alignemt shows the output of Jpred3. The secondary structure elements is marked by ourself. It predicted 14 alpha-helices and 15 beta-sheets. |
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| + | 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. |
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| − | [[File:jpred_pic.png|thumb|center| Jpred output with colored secondary structure elements]] |
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| + | [[File:jpred_pic.png|thumb|center| Figure 4: Jpred output with colored secondary structure elements]] |
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| − | === 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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473 - 492 A A A AA A AA AA |
473 - 492 A A A AA A AA AA |
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| − | === Discussion === |
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| − | To determine how succesful our secondary structure prediction with PSIPRED and Jpred are, we had to compare it with the secondary structure assignment of DSSP. First of all, DSSP assigns no beta-sheets whereas both prediction methods predict some beta-sheets. Therefore the main comparison in this case refers to the alpha-helices. |
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| − | For PSIPRED the prediction of the alpha-helices was good. In the most cases the alpha-helices of DSSP und PSIPRED corrspond. There is only one helix which is predicted by PSIPRED which is not assigned as helix by DSSP. Furthermore there are three helices which are allocated as helices by DSSP which were not predicted by PSIPRED. The most of these helices which were presented only in one output are very small ones. |
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| − | For Jpred3 the prediction of the alpha-helices was sufficiently good. In the most cases it agrees with DSSP. There are only two helices which are predicted by Jpred and which are not also assigned by DSSP. In contrary there are three small helics which are allocated to an alpha-helices by DSSP but are not predicted by Jpred. There is another special case where DSSP assignes two helices which are separated by a turn and Jpred predicts there only one big helix. |
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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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| − | All in all, the prediction of the helices is probably good because they correspond mostly with the assignmet of DSSP. The only negative aspect is, that both prediction methods predict a lot of sheets which were not assigned by DSSP at all. |
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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
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473 - 492 RRGVQAQPLNVGFCEQEFEQ
473 - 492 HTT TTT TT
473 - 492
473 - 492 A A A AA A AA AA
Back to [Sequence-based Prediction]
