NINE :
 
 
 
4A4 +
4A5 +
4AA7 +
4B3 +
4B9 +
4E.4 +
4E.6 +
4G1 +
4W1 +
4G5 +
4G6 +
4I1 +
4I4 +
4J2 +
4J9 +
4K12 +
4K8 +
4L4 +
4L6 +
4M5 +
4Z12 +
4Z5 +
4Z6 +
4P9 +
4Q2 +
4Q4 +
4R10 +
4R12 +
4R5 +
4S12 +
4T11 ?
4T4 +
4V7 ?
4Z9 +

: DATA
 
 
 
DBONDSINTHEMEMORYOFTHECOMPUTER;AND(3)ANEWTHREE-DIMENSIONALGRAPHICSINTE
RIBED'INTOANIN-MEMORYDATASTRUCTURE,'TRANSLATED'INTOTHEMMDB-APIMOLECULA
ELAY 19-merdnadoublehelix(1d66;ref.6),showninfig2.thisstructurecontainsdna,
REE- cn3dusesdatafromthemmdb,whichisinadifferentformatfrompdbdatabaseentrie
YUND pdbdatafiles,mmdbdatafileshaveaconsistentinterpretationandcn3dassumest
S1.1 stservice(box1)allowsonetoretrievealistofallstructurallysimilarprotein
WERT allyinterestingcontentsofastructuredatabasefile.someofthenewcontentadd
PROC dwithhollowcylinders.tocontrastwiththeprotein,thecompletestructureofth
SDIR ednamoleculeisshown,coloredwithacpkcolorscheme.thezn2+ionsareshownasme
RSTR edintommdbdatafilesincludesthesecondarystructuredefinitionsanddomainin
HICS formationasusedinthevaststructure-structurecomparision[7]service.theva
N3D2 hatthedescriptionofatomsandbondswithinthemmdbdatafileiscorrectandthatn
N.1I iththecharacteristichemeringemphasizedwithabrightorangeironsphereandbo
INGT imensionalstructuredatabecomeseasier,asonecanimmediatelyseethebiologic
WARE lassicproteinsuchaswatsonandkendrew'smyoglobin(1mbn)intocn3d,yougetani
ROPO magethatresemblesthetextbookpicture,showingsecondarystructuretogetherw
VIDE ospecialexceptionhandlingisrequiredforroguedatafiles.thuswhenyouloadac
ING. oftheproteincoloredbysecondarystructure,withthealpha-heliceshighlighte
UPDA proteinandzn2+ions.thedefaultcn3dimageshowsanalpha-carbonbackbonetrace
TOTH s.convertingfilesintommdbformatrequiresextensivevalidation,makingtheda
OVID stoanyproteininthemmdbdatabase,anditalsoprovidesthree-dimensionalstruc
SELE tamorereliableforsoftwarethatmakesthree-dimensionalimages.bycontrastto
TEXT tallicspheres.smarterdefaultimagesmeanthatstudyingthecontentsofthree-d
CN3D turedatafilestoviewthesuperpositionsofsimilarproteinsinavarietyoffilef
,TRA undoxygen.anexampleofthedefaultcn3dviewisthatofthestructureofgal4witha
INGIMAGEUPDATERATEISFASTENOUGHTOPROVIDEAVERYFLUIDROTATIONONTHECURRENTC
RATIONSANDMOVEMENTSCANBEALTEREDALLOWINGALTERNATIVEMOUSEBEHAVIORSSUCHAS
FORMAT.INADDITION,CN3D2.0ISINCORPORATINGASTRUCTURE-SUPERPOSITIONMODEMA
MDB-API,THEMIDDLELAYEROFCN3D,REPRESENTINGTHEMOLECULARSTRUCTURE;THISPRO
ILLBEUSEDMOREEXTENSIVELYINCN3D2.0,SUCHASPOINT-AND-CLICKSELECTION,ALLOW
SWILLBEIMPLEMENTEDUSINGTHISMECHANISMINCN3D2.0.THELARGESTIMPROVEMENTINC
RE-FEATURE'FILE.THISWILLALLOWCN3DUSERSTOMAKEILLUSTRATIONSANDANNOTATION
KINGITTHEPREFERREDBROWSEROFVAST[7]STRUCTURE-STRUCTURESUPERPOSITIONS,EV
RFACECALLEDVIEWER3D.OFTHESE,THEMOSTOBVIOUSISTHEVIEWER3DTHREE-DIMENSION
XY,YZORXZROTATIONS.NEWFEATURESLIKETHREE-DIMENSIONALDISTANCEMEASUREMENT
STHEMBACKOUTINTOFILES;(2)ANEWMOLECULARPROGRAMMINGINTERFACELAYERCALLEDM
VIDEODISPLAYCOLORPALETTEINTOCONTINUOUSSHADESFORTHREE-DIMENSIONALRENDER
LLBEABLETOEXCHANGEINFORMATIONWITHOUTBECOMINGEXPERTSINTHEUNDERLYINGFILE
ALGRAPHICSPRESENTATIONLAYER.THISLAYERISUSEDTOMAKEPICTURESCOMPOSEDOF'TH
ENPROVIDING'ANIMATED'VIEWSOFPROTEINSTRUCTUREEVOLUTION.             PbN

<FONT color=#D05050 size=1>
  <CODE>
    <FONT color=#808080>
      DBONDSINTHEMEMORYOFTHECOMPUTER;AND(3)ANEWTHREE-DIMENSIONALGRAPHICSINTE<br>
      RIBED'INTOANIN-MEMORYDATASTRUCTURE,'TRANSLATED'INTOTHEMMDB-APIMOLECULA<br>
      ELAY</FONT></CODE>
  19-merdnadoublehelix(1d66;ref.6),showninfig2.thisstructurecontainsdna,<br>
  <CODE>
    <FONT color=#808080>
      REE-</FONT></CODE>
  cn3dusesdatafromthemmdb,whichisinadifferentformatfrompdbdatabaseentrie<br>
  <CODE>
    <FONT color=#808080>
      YUND</FONT></CODE>
  pdbdatafiles,mmdbdatafileshaveaconsistentinterpretationandcn3dassumest<br>
  <CODE>
    <FONT color=#808080>
      S1.1</FONT></CODE>
  stservice(box1)allowsonetoretrievealistofallstructurallysimilarprotein<br>
  <CODE>
    <FONT color=#808080>
      WERT</FONT></CODE>
  allyinterestingcontentsofastructuredatabasefile.someofthenewcontentadd<br>
  <CODE>
    <FONT color=#808080>
      PROC</FONT></CODE>
  dwithhollowcylinders.tocontrastwiththeprotein,thecompletestructureofth<br>
  <CODE>
    <FONT color=#808080>
      SDIR</FONT></CODE>
  ednamoleculeisshown,coloredwithacpkcolorscheme.thezn2+ionsareshownasme<br>
  <CODE>
    <FONT color=#808080>
      RSTR</FONT></CODE>
  edintommdbdatafilesincludesthesecondarystructuredefinitionsanddomainin<br>
  <CODE>
    <FONT color=#808080>
      HICS</FONT></CODE>
  formationasusedinthevaststructure-structurecomparision[7]service.theva<br>
  <CODE>
    <FONT color=#808080>
      N3D2</FONT></CODE>
  hatthedescriptionofatomsandbondswithinthemmdbdatafileiscorrectandthatn<br>
  <CODE>
    <FONT color=#808080>
      N.1I</FONT></CODE>
  iththecharacteristichemeringemphasizedwithabrightorangeironsphereandbo<br>
  <CODE>
    <FONT color=#808080>
      INGT</FONT></CODE>
  imensionalstructuredatabecomeseasier,asonecanimmediatelyseethebiologic<br>
  <CODE>
    <FONT color=#808080>
      WARE</FONT></CODE>
  lassicproteinsuchaswatsonandkendrew'smyoglobin(1mbn)intocn3d,yougetani<br>
  <CODE>
    <FONT color=#808080>
      ROPO</FONT></CODE>
  magethatresemblesthetextbookpicture,showingsecondarystructuretogetherw<br>
  <CODE>
    <FONT color=#808080>
      VIDE</FONT></CODE>
  ospecialexceptionhandlingisrequiredforroguedatafiles.thuswhenyouloadac<br>
  <CODE>
    <FONT color=#808080>
      ING.</FONT></CODE>
  oftheproteincoloredbysecondarystructure,withthealpha-heliceshighlighte<br>
  <CODE>
    <FONT color=#808080>
      UPDA</FONT></CODE>
  proteinandzn2+ions.thedefaultcn3dimageshowsanalpha-carbonbackbonetrace<br>
  <CODE>
    <FONT color=#808080>
      TOTH</FONT></CODE>
  s.convertingfilesintommdbformatrequiresextensivevalidation,makingtheda<br>
  <CODE>
    <FONT color=#808080>
      OVID</FONT></CODE>
  stoanyproteininthemmdbdatabase,anditalsoprovidesthree-dimensionalstruc<br>
  <CODE>
    <FONT color=#808080>
      SELE</FONT></CODE>
  tamorereliableforsoftwarethatmakesthree-dimensionalimages.bycontrastto<br>
  <CODE>
    <FONT color=#808080>
      TEXT</FONT></CODE>
  tallicspheres.smarterdefaultimagesmeanthatstudyingthecontentsofthree-d<br>
  <CODE>
    <FONT color=#808080>
      CN3D</FONT></CODE>
  turedatafilestoviewthesuperpositionsofsimilarproteinsinavarietyoffilef<br>
  <CODE>
    <FONT color=#808080>
      ,TRA</FONT></CODE>
  undoxygen.anexampleofthedefaultcn3dviewisthatofthestructureofgal4witha<br>
  <CODE>
    <FONT color=#808080>
      INGIMAGEUPDATERATEISFASTENOUGHTOPROVIDEAVERYFLUIDROTATIONONTHECURRENTC<br>
      RATIONSANDMOVEMENTSCANBEALTEREDALLOWINGALTERNATIVEMOUSEBEHAVIORSSUCHAS<br>
      FORMAT.INADDITION,CN3D2.0ISINCORPORATINGASTRUCTURE-SUPERPOSITIONMODEMA<br>
      MDB-API,THEMIDDLELAYEROFCN3D,REPRESENTINGTHEMOLECULARSTRUCTURE;THISPRO<br>
      ILLBEUSEDMOREEXTENSIVELYINCN3D2.0,SUCHASPOINT-AND-CLICKSELECTION,ALLOW<br>
      SWILLBEIMPLEMENTEDUSINGTHISMECHANISMINCN3D2.0.THELARGESTIMPROVEMENTINC<br>
      RE-FEATURE'FILE.THISWILLALLOWCN3DUSERSTOMAKEILLUSTRATIONSANDANNOTATION<br>
      KINGITTHEPREFERREDBROWSEROFVAST[7]STRUCTURE-STRUCTURESUPERPOSITIONS,EV<br>
      RFACECALLEDVIEWER3D.OFTHESE,THEMOSTOBVIOUSISTHEVIEWER3DTHREE-DIMENSION<br>
      XY,YZORXZROTATIONS.NEWFEATURESLIKETHREE-DIMENSIONALDISTANCEMEASUREMENT<br>
      STHEMBACKOUTINTOFILES;(2)ANEWMOLECULARPROGRAMMINGINTERFACELAYERCALLEDM<br>
      VIDEODISPLAYCOLORPALETTEINTOCONTINUOUSSHADESFORTHREE-DIMENSIONALRENDER<br>
      LLBEABLETOEXCHANGEINFORMATIONWITHOUTBECOMINGEXPERTSINTHEUNDERLYINGFILE<br>
      ALGRAPHICSPRESENTATIONLAYER.THISLAYERISUSEDTOMAKEPICTURESCOMPOSEDOF'TH<br>
      ENPROVIDING'ANIMATED'VIEWSOFPROTEINSTRUCTUREEVOLUTION.
      &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;PbN<br>
      <FONT color=#D05050 size=2>
      
        FORMATREQUIRESEXTENSIVEVALIDATION
      
      </FONT>
      <FONT size=3>
        formatrequiresextensivevalidation</FONT><br>
    </FONT>
  </CODE>
</FONT>
formatrequiresextensivevalidation
  
 
 
 
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