SWISS-MODEL - Workspace - Model SWISS-MODEL - Workspace - Model Results - Drosophilla Melanogasterresults - Drosophilla Melanogaster

6/24/2015
SWISSMODEL|Workspace|ModelResults|ny9NPC
SWISSMODELHomologyModelingReport
ModelBuildingReport
Thisdocumentliststheresultsforthehomologymodelingproject"UntitledProject"submittedtoSWISSMODELworkspaceonJune
24,2015,2:19a.m..ThesubmittedprimaryaminoacidsequenceisgiveninTableT1.
Ifyouuseanyresultsinyourresearch,pleasecitetherelevantpublications:
MarcoBiasiniStefanBienertAndrewWaterhouseKonstantinArnoldGabrielStuderTobiasSchmidtFlorianKieferTizianoGallo
CassarinoMartinoBertoniLorenzaBordoliTorstenSchwede.(2014).SWISSMODEL:modellingproteintertiaryandquaternary
structureusingevolutionaryinformation.NucleicAcidsResearch(1July2014)42(W1):W252W258doi:10.1093/nar/gku340.
Arnold,K.,Bordoli,L.,Kopp,J.andSchwede,T.(2006)TheSWISSMODELworkspace:awebbasedenvironmentforprotein
structurehomologymodelling.Bioinformatics,22,195201.
Benkert,P.,Biasini,M.andSchwede,T.(2011)Towardtheestimationoftheabsolutequalityofindividualproteinstructuremodels.
Bioinformatics,27,343350
Results
TheSWISSMODELtemplatelibrary(SMTLversion20150617,PDBrelease20150612)wassearchedwithBlast(Altschuletal.,
1997)andHHBlits(Remmert,etal.,2011)forevolutionaryrelatedstructuresmatchingthetargetsequenceinTableT1.Fordetailson
thetemplatesearch,seeMaterialsandMethods.Overall84templateswerefound(TableT2).
Models
Nomodelshavebeenbuiltforthisproject.
MaterialsandMethods
TemplateSearch
TemplatesearchwithBlastandHHBlitshasbeenperformedagainsttheSWISSMODELtemplatelibrary(SMTL,lastupdate:2015
0617,lastincludedPDBrelease:20150612).
ThetargetsequencewassearchedwithBLAST(Altschuletal.,1997)againsttheprimaryaminoacidsequencecontainedinthe
SMTL.Atotalof42templateswerefound.
AninitialHHblitsprofilehasbeenbuiltusingtheprocedureoutlinedin(Remmert,etal.,2011),followedby1iterationofHHblits
againstNR20.TheobtainedprofilehasthenbesearchedagainstallprofilesoftheSMTL.Atotalof43templateswerefound.
TemplateSelection
Foreachidentifiedtemplate,thetemplate'squalityhasbeenpredictedfromfeaturesofthetargettemplatealignment.Thetemplates
withthehighestqualityhavethenbeenselectedformodelbuilding.
ModelBuilding
ModelsarebuiltbasedonthetargettemplatealignmentusingPromodII.Coordinateswhichareconservedbetweenthetargetandthe
templatearecopiedfromthetemplatetothemodel.Insertionsanddeletionsareremodeledusingafragmentlibrary.Sidechainsare
thenrebuilt.Finally,thegeometryoftheresultingmodelisregularizedbyusingaforcefield.IncaseloopmodellingwithProModII
(Guex,etal.,1997)doesnotgivesatisfactoryresults,analternativemodelisbuiltwithMODELLER(Sali,etal.,1993).
ModelQualityEstimation
TheglobalandperresiduemodelqualityhasbeenassessedusingtheQMEANscoringfunction(Benkert,etal.,2011).Forimproved
performance,weightsoftheindividualQMEANtermshavebeentrainedspecificallyforSWISSMODEL.
LigandModeling
Ligandspresentinthetemplatestructurearetransferredbyhomologytothemodelwhenthefollowingcriteriaaremet(Gallo
Casserino,tobepublished):(a)Theligandsareannotatedasbiologicallyrelevantinthetemplatelibrary,(b)theligandisincontact
withthemodel,(c)theligandisnotclashingwiththeprotein,(d)theresiduesincontactwiththeligandareconservedbetweenthe
targetandthetemplate.Ifanyofthesefourcriteriaisnotsatisfied,acertainligandwillnotbeincludedinthemodel.Themodel
summaryincludesinformationonwhyandwhichligandhasnotbeenincluded.
OligomericStateConservation
Homooligomericstructureofthetargetproteinispredictedbasedontheanalysisofpairwiseinterfacesoftheidentifiedtemplate
structures.Foreachrelevantinterfacebetweenpolypetidechains(interfaceswithmorethan10residueresidueinteractions),the
http://swissmodel.expasy.org/interactive/ny9NPC/models/report.html
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6/24/2015
QscoreOligomer(Marianietal.,2011)ispredictedfromfeaturessuchassimilaritytotargetandfrequencyofobservingthisinterface
intheidentifiedtemplates(Kiefer,Bertoni,Biasini,tobepublished).Thepredictionisperformedwitharandomforestregressorusing
thesefeaturesasinputparameterstopredicttheprobabilityofconservationforeachinterface.TheQscoreOligomerofthewhole
complexisthencalculatedastheweightaveragedQscoreOligomeroftheinterfaces.Theoligomericstateofthetargetispredictedto
bethesameasinthetemplatewhenQscoreOligomerispredictedtobehigherorequalto0.5.
References
Altschul,S.F.,Madden,T.L.,Schaffer,A.A.,Zhang,J.,Zhang,Z.,Miller,W.andLipman,D.J.(1997)GappedBLASTandPSI
BLAST:anewgenerationofproteindatabasesearchprograms.NucleicAcidsRes,25,33893402.
Remmert,M.,Biegert,A.,Hauser,A.andSoding,J.(2012)HHblits:lightningfastiterativeproteinsequencesearchingbyHMMHMM
alignment.NatMethods,9,173175.
Guex,N.andPeitsch,M.C.(1997)SWISSMODELandtheSwissPdbViewer:anenvironmentforcomparativeproteinmodeling.
Electrophoresis,18,27142723.
Sali,A.andBlundell,T.L.(1993)Comparativeproteinmodellingbysatisfactionofspatialrestraints.JMolBiol,234,779815.
Benkert,P.,Biasini,M.andSchwede,T.(2011)Towardtheestimationoftheabsolutequalityofindividualproteinstructuremodels.
Bioinformatics,27,343350.
Mariani,V.,Kiefer,F.,Schmidt,T.,Haas,J.andSchwede,T.(2011)Assessmentoftemplatebasedproteinstructurepredictionsin
CASP9.Proteins,79Suppl10,3758.
TableT1:
Primaryaminoacidsequenceforwhichtemplatesweresearchedandmodelswerebuilt.
MRLFLLALLATLAVTQALVKEEIQAKEYLENLNKELAKRTNVETEAAWAYGSNITDENEKKKNEISAELAKFMKEVASDTTKFQWRSYQSEDLKRQFKAL
TKLGYAALPEDDYAELLDTLSAMESNFAKVKVCDYKDSTKCDLALDPEIEEVISKSRDHEELAYYWREFYDKAGTAVRSQFERYVELNTKAAKLNNFTSG
AEAWLDEYEDDTFEQQLEDIFADIRPLYQQIHGYVRFRLRKHYGDAVVSETGPIPMHLLGNMWAQQWSEIADIVSPFPEKPLVDVSAEMEKQGYTPLKMF
QMGDDFFTSMNLTKLPQDFWDKSIIEKPTDGRDLVCHASAWDFYLTDDVRIKQCTRVTQDQLFTVHHELGHIQYFLQYQHQPFVYRTGANPGFHEAVGDV
LSLSVSTPKHLEKIGLLKDYVRDDEARINQLFLTALDKIVFLPFAFTMDKYRWSLFRGEVDKANWNCAFWKLRDEYSGIEPPVVRSEKDFDAPAKYHISA
DVEYLRYLVSFIIQFQFYKSACIKAGQYDPDNVELPLDNCDIYGSAAAGAAFHNMLSMGASKPWPDALEAFNGERIMSGKAIAEYFEPLRVWLEAENIKN
NVHIGWTTSNKCVSS
TableT2:
Template
Seq
Found
Seq
Oligostate
Method Resolution
Coverage
Identity
by
Similarity
2x94.1.A
100.00
monomer HHblits
Xray
1.88
0.62
0.97
ANGIOTENSINCONVERTINGENZYME
2x91.1.A
100.00
monomer HHblits
Xray
1.98
0.62
0.97
2x94.1.A
100.00
monomer
BLAST
Xray
1.88
0.62
0.97
2x91.1.A
100.00
monomer
BLAST
Xray
1.98
0.62
0.97
1j36.1.A
99.00
monomer HHblits
Xray
2.40
0.61
0.97
angiotensinconvertingenzyme
1j36.1.A
98.99
monomer
BLAST
Xray
2.40
0.61
0.97
angiotensinconvertingenzyme
4c2n.1.A
44.90
monomer HHblits
Xray
2.59
0.42
0.96
1uze.1.A
44.90
monomer HHblits
Xray
1.82
0.42
0.96
4apj.1.A
44.90
hetero
oligomer
HHblits
Xray
2.60
0.42
0.96
2ydm.1.A
44.90
monomer HHblits
Xray
2.44
0.42
0.96
2oc2.1.A
44.90
monomer HHblits
Xray
2.25
0.42
0.96
Angiotensinconvertingenzyme,somatic
isoform
2iux.1.A
44.90
monomer HHblits
Xray
2.80
0.42
0.96
Description
2iul.1.A
44.90
monomer HHblits
Xray
2.01
0.42
0.96
4c2p.1.A
44.73
monomer HHblits
Xray
1.99
0.42
0.96
4c2r.1.A
44.73
monomer HHblits
Xray
2.30
0.42
0.96
4c2o.1.A
44.73
monomer HHblits
Xray
1.80
0.42
0.96
3bkl.1.A
44.73
monomer HHblits
Xray
2.18
0.42
0.96
isoform
2xy9.1.A
44.86
monomer HHblits
Xray
1.97
0.42
0.95
4bzs.1.A
40.88
monomer HHblits
Xray
2.10
0.41
0.96
2c6f.1.A
41.12
monomer HHblits
Xray
3.01
0.41
0.96
ANGIOTENSINCONVERTINGENZYME,
SOMATICISOFORM
2iul.1.A
45.09
monomer
BLAST
Xray
2.01
0.43
0.94
2xy9.1.A
45.09
monomer
BLAST
Xray
1.97
0.43
0.94
2ydm.1.A
45.09
monomer
BLAST
Xray
2.44
0.43
0.94
hetero
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6/24/2015
4apj.1.A
45.09
oligomer
BLAST
Xray
2.60
0.43
0.94
1uze.1.A
45.09
monomer
BLAST
Xray
1.82
0.43
0.94
2oc2.1.A
45.09
monomer
BLAST
Xray
2.25
0.43
0.94
isoform
4c2n.1.A
45.09
monomer
BLAST
Xray
2.59
0.43
0.94
2iux.1.A
45.09
monomer
BLAST
Xray
2.80
0.43
0.94
4c2p.1.A
44.92
monomer
BLAST
Xray
1.99
0.43
0.94
4c2r.1.A
44.92
monomer
BLAST
Xray
2.30
0.43
0.94
3bkl.1.A
44.92
monomer
BLAST
Xray
2.18
0.42
0.94
isoform
4c2o.1.A
44.92
monomer
BLAST
Xray
1.80
0.42
0.94
2xyd.1.A
40.78
monomer HHblits
Xray
2.15
0.41
0.96
3nxq.1.A
40.85
monomer HHblits
Xray
1.99
0.41
0.96
Angiotensinconvertingenzyme
2c6f.1.A
42.66
monomer
BLAST
Xray
3.01
0.42
0.94
ANGIOTENSINCONVERTINGENZYME,
SOMATICISOFORM
4bzs.1.A
42.49
monomer
BLAST
Xray
2.10
0.42
0.94
1r4l.1.A
36.39
hetero
oligomer
HHblits
Xray
3.00
0.39
0.96
angiotensinIconvertingenzyme2
1r42.1.A
36.39
hetero
oligomer
HHblits
Xray
2.20
0.39
0.96
3d0i.1.B
36.47
hetero
oligomer
HHblits
Xray
2.90
0.39
0.95
Angiotensinconvertingenzyme2
3d0i.1.A
36.47
hetero
oligomer
HHblits
Xray
2.90
0.39
0.95
2ajf.1.A
36.54
hetero
oligomer
HHblits
Xray
2.90
0.39
0.95
AngiotensinconvertingenzymeRelated
Carboxypeptidase(Ace2)
2ajf.2.A
36.54
hetero
oligomer
HHblits
Xray
2.90
0.39
0.95
3kbh.1.A
36.54
hetero
oligomer
HHblits
Xray
3.31
0.39
0.95
3scl.1.A
36.72
hetero
oligomer
HHblits
Xray
3.00
0.40
0.94
Angiotensinconvertingenzyme2chimera
3scl.2.A
36.72
hetero
oligomer
HHblits
Xray
3.00
0.40
0.94
3sci.2.A
36.72
hetero
oligomer
HHblits
Xray
2.90
0.39
0.94
3sci.1.A
36.72
hetero
oligomer
HHblits
Xray
2.90
0.39
0.94
1r4l.1.A
37.67
hetero
oligomer
BLAST
Xray
3.00
0.40
0.94
1r42.1.A
37.67
hetero
oligomer
BLAST
Xray
2.20
0.40
0.94
3sci.1.A
37.67
hetero
oligomer
BLAST
Xray
2.90
0.40
0.94
3sci.2.A
37.67
hetero
oligomer
BLAST
Xray
2.90
0.40
0.94
3kbh.1.A
37.67
hetero
oligomer
BLAST
Xray
3.31
0.40
0.94
2ajf.2.A
37.67
hetero
oligomer
BLAST
Xray
2.90
0.40
0.94
2ajf.1.A
37.67
hetero
oligomer
BLAST
Xray
2.90
0.40
0.94
3d0i.1.B
37.70
hetero
oligomer
BLAST
Xray
2.90
0.40
0.93
3d0i.1.A
37.70
hetero
oligomer
BLAST
Xray
2.90
0.40
0.93
3scl.2.A
37.70
hetero
oligomer
BLAST
Xray
3.00
0.40
0.93
3scl.1.A
37.70
hetero
oligomer
BLAST
Xray
3.00
0.40
0.93
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3nxq.1.A
43.86
monomer
BLAST
Xray
1.99
0.43
0.90
Angiotensinconvertingenzyme
2xyd.1.A
43.86
monomer
BLAST
Xray
2.15
0.43
0.90
NEUROLYSIN
1i1i.1.A
17.25
monomer HHblits
Xray
2.30
0.28
0.84
2o3e.1.A
17.05
monomer HHblits
Xray
2.20
0.28
0.84
Neurolysin
4ka7.1.A
16.38
monomer HHblits
Xray
1.80
0.27
0.84
OligopeptidaseA
1s4b.1.A
16.09
monomer HHblits
Xray
2.00
0.28
0.84
Thimetoligopeptidase
4fxy.1.A
17.15
monomer HHblits
Xray
2.80
0.28
0.83
Neurolysin,mitochondrial
2o36.1.A
15.50
monomer HHblits
Xray
1.95
0.28
0.84
Thimetoligopeptidase
4ka8.1.A
16.99
monomer HHblits
Xray
1.90
0.28
0.83
OligopeptidaseA
4put.1.A
16.99
monomer HHblits
Xray
3.00
0.28
0.83
CytosolicoligopeptidaseA
1y79.1.A
15.91
monomer HHblits
Xray
2.00
0.27
0.83
PeptidylDipeptidaseDcp
2qr4.1.A
14.17
homodimer HHblits
Xray
2.50
0.28
0.81
PeptidaseM3B,oligoendopeptidaseF
2qr4.1.B
14.17
homodimer HHblits
Xray
2.50
0.28
0.81
PeptidaseM3B,oligoendopeptidaseF
3ahm.1.A
13.97
monomer HHblits
Xray
2.00
0.28
0.81
Oligopeptidase
3sks.1.A
14.29
monomer HHblits
Xray
2.05
0.28
0.81
PutativeOligoendopeptidaseF
2h1n.1.A
14.23
monomer HHblits
Xray
3.00
0.28
0.81
OligoendopeptidaseF
3ce2.1.A
13.32
monomer HHblits
Xray
2.60
0.27
0.82
Putativepeptidase
3hq2.1.A
16.92
homodimer HHblits
Xray
2.90
0.29
0.75
BacillussubtilisM32carboxypeptidase
3dwc.1.A
17.06
homodimer HHblits
Xray
2.10
0.29
0.75
Metallocarboxypeptidase
1wgz.3.A
17.11
monomer HHblits
Xray
2.60
0.29
0.74
carboxypeptidase1
1wgz.2.A
17.11
monomer HHblits
Xray
2.60
0.29
0.74
carboxypeptidase1
1wgz.1.A
17.11
monomer HHblits
Xray
2.60
0.29
0.74
carboxypeptidase1
3hoa.1.A
16.92
homodimer HHblits
Xray
2.10
0.29
0.74
Thermostablecarboxypeptidase1
1k9x.2.A
15.10
homodimer HHblits
Xray
2.30
0.28
0.74
M32carboxypeptidase
1ka4.1.A
15.10
homodimer HHblits
Xray
3.00
0.28
0.74
M32carboxypeptidase
4l7a.1.A
31.25
monomer HHblits
Xray
2.09
0.39
0.03
Uncharacterizedprotein
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