Difference between revisions of "Glucocerebrosidase sequence based prediction"
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=== General === |
=== General === |
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| + | The secondary structure of a protein is the three-dimensional form. In contrast to the tertiary structure it describes the local segments. Because of weak chemical forces like hydrogen bonds and the values of the φ and ψ angles they form different structures. The main types are α-helices and parallel and anti-parallel β-sheets. Some rare structures are π-helices and 3,10-helices. Another possibility are coils, which are irregular formed elements.<br/> |
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| + | A protein consists of several secondary structure elements which build together the tertiary structure. <ref>http://en.wikipedia.org/wiki/Biomolecular_structure#Secondary_structure</ref> |
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| + | [[File:glucocerebrosidase_secondary_structure.gif||thumb||beta sheets and a α-helix as examples for secondary structure <ref>http://www.nature.com/horizon/proteinfolding/background/images/importance_f3.gif</ref>]] |
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=== PSIPRED === |
=== PSIPRED === |
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Revision as of 10:53, 27 May 2011
Contents
Secondary structure prediction
General
The secondary structure of a protein is the three-dimensional form. In contrast to the tertiary structure it describes the local segments. Because of weak chemical forces like hydrogen bonds and the values of the φ and ψ angles they form different structures. The main types are α-helices and parallel and anti-parallel β-sheets. Some rare structures are π-helices and 3,10-helices. Another possibility are coils, which are irregular formed elements.
A protein consists of several secondary structure elements which build together the tertiary structure. <ref>http://en.wikipedia.org/wiki/Biomolecular_structure#Secondary_structure</ref>
PSIPRED
PSIPRED is a method by David T. Jones, published 1999 in JMB with "Protein Secondary Structure Prediction Based on Position-specific Scoring Matrices". PSIPRED works with a two-stage neural network to predict secondary structure. These are based on the position specific scoring matrices generated by PSI-BLAST, which is run before.<ref>David T. Jones, Protein Secondary Structure Prediction Based on Position-specific Scoring Matrices, JMB, 1999</ref>
We run the online and the local version of PSIPRED and got different results. In the following it is compared to the secondary structure given in Uniprot<ref>http://www.uniprot.org/uniprot/P04062</ref>.
| Conf: | 988898954488887622315999999999998641038968865325999649995388
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| online: | CCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEECCC
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| Conf: | 987898955489988742200466888998986410038977877777863169974474
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| local: | CCCCCCCCCCCCCCCCCEEEEHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEEECCC
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| uniprot: | ------------------------------------------------EEEE-EEEEEE-
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| AA: | MEFSSPSREECPKPLSRVSIMAGSLTGLLLLQAVSWASGARPCIPKSFGYSSVVCVCNAT
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| Conf: | 558889998889992599996377885421237645688875108995378301079247
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| online: | CCCCCCCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCCEEEECCCCCEEEEEEE
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| Conf: | 148899998788875431100345640022100111177897107840966454557422
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| local: | CCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCEEEECCCCCCCEEEEE
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| uniprot: | -------------EEEEEEEE-----EEEEEEE-EEE----EEEEEEEEEEEEEE--EEE
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| AA: | YCDSFDPPTFPALGTFSRYESTRSGRRMELSMGPIQANHTGTGLLLTLQPEQKFQKVKGF
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| Conf: | 300233899997249999999999860597882105999750588999986666899999
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| online: | EECCCHHHHHHHHCCCHHHHHHHHHHCCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCCC
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| Conf: | 011335889987508927898998851396893001358621344677653324799999
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| local: | CCCCCHHHHHHHHHCCHHHHHHHHHHHCCCCCCEEEEEEEECCCCCCCCCCCCCCCCCCC
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| uniprot: | EE--HHHHHHH----HHHHHHHHHHHH-CCCC---EEEEEEE--EEEEE------EEE--
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| AA: | GGAMTDAAALNILALSPPAQNLLLKSYFSEEGIGYNIIRVPMASCDFSIRTYTYADTPDD
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| Conf: | 689999994100245289999999971999389971377785612147247999889999
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| online: | CCCCCCCCCHHCCCCCHHHHHHHHHHCCCCCEEEECCCCCCCCCEECCCCCCCCCCCCCC
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| Conf: | 721111368543220024799998733999689957899974220056347854325899
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| local: | CCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCCC
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| uniprot: | --------HHHH--HHHHHHHHHHH-----EEEEEEE---HHH----EEEEE-EEEE---
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| AA: | FQLHNFSLPEEDTKLKIPLIHRALQLAQRPVSLLASPWTSPTWLKTNGAVNGKGSLKGQP
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| Conf: | 922699999999999999975490786872012579899999999986349999999999
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| online: | CCHHHHHHHHHHHHHHHHHHHCCEEEEEEECCCCCCCCCCCCCCCCCCCCCHHHHHHHHH
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| Conf: | 971468799999999967663395143898112789787678873222114422121122
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| local: | CCHHHHHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCHHHH
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| uniprot: | -HHHHHHHHHHHHHHHHHHH-----EEEEE-----HHH------------HHHHHHHHHH
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| AA: | GDIYHQTWARYFVKFLDAYAEHKLQFWAVTAENEPSAGLLSGYPFQCLGFTPEHQRDFIA
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| Conf: | 955799851689972999944888873334664149955640224689831699998033
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| online: | HHHHHHHHCCCCCCEEEEEECCCCCCHHHHHHHHCCCHHHHCCCCEEEEEECCCCCCHHH
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| Conf: | 111332310577410134212544556520222238976651151878702212236320
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| local: | HHHHHHHHCCCCCCCEEEEECCCCCCCCCCHHHHCCCHHHHHCCEEEEEECCCCCCCCCC
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| uniprot: | -HHHHHH--CCCCEEEEEEEEEHHH--HHHHHHH--HHHH----EEEEEEE------HHH
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| AA: | RDLGPTLANSTHHNVRLLMLDDQRLLLPHWAKVVLTDPEAAKYVHGIAVHWYLDFLAPAK
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| Conf: | 412688750999509994343699998866567831444255999999996402335772
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| online: | HHHHHHHHCCCCCEEEEECCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCEEEEEE
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| Conf: | 011111126898001101210389653344579861210143212566552001100000
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| local: | CCCCCCCCCCCCCCEEHHHHCCCCCCCCCCCCCCCHHHHCCCCHHHHHHHHHHHHHHEEE
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| uniprot: | HHHHHHHH---EEEEEEEEE--------------HHHHHHHHHHHHHHHH--EEEEEEEE
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| AA: | ATLGETHRLFPNTMLFASEACVGSKFWEQSVRLGSWDRGMQYSHSIITNLLYHVVGWTDW
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| Conf: | 000169999986689878535895679769986202333102244469939999542389
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| online: | EECCCCCCCCCCCCCCCCCCEEEECCCCEEEECCHHHHHHHHCCCCCCCCEEEEEEECCC
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| Conf: | 023699999860001325228998208703226821232123444679927984435078
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| local: | CCCCCCCCCCCCEECCCCCCEEEEECCCCEEECCCEEEECCCCCCCCCCCEEEEEEEECC
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| uniprot: | E-----------------EEEEEHHH-EEEE-HHHHHHHHHH-------EEEEEEEEE--
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| AA: | NLALNPEGGPNWVRNFVDSPIIVDITKDTFYKQPMFYHLGHFSKFIPEGSQRVGLVASQK
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| Conf: | 99028999928998999999099993779999099304998518951899999309
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| online: | CCCEEEEEECCCCCEEEEEECCCCCCEEEEEEECCCCEEEEECCCCEEEEEEEEEC
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| Conf: | 99538995649997799999146898214741998642000389842568774139
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| local: | CCCCEEEEECCCCCEEEEEEECCCCCEEEEECCCCCCCCCCCCCCCEEEEEEEECC
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| uniprot: | EEEEEEEE-----EEEEEEE-EEE-EEEEEEECCCEEEEEEE---EEEEEEE----
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| AA: | NDLDAVALMHPDGSAVVVVLNRSSKDVPLTIKDPAVGFLETISPGYSIHTYLWRRQ
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The results differ a lot. The online version of PSIPRED seems to have different parameters than the local version. So we got different results. Compared to the given secondary structure in Uniprot there are many regions that are predicted wrong.
