Modeller_doc_japanese_ver.1.0

This is a Japanese manual of MODELLER. MODELLER is used for homology or comparative modeling of protein three-dimensional structures.

Transcript

1. 1
   120811 ver. 1.0
   Presented by Satoshi Kume, Osaka Pref. Univ.
   MODELLER Protocol on Mac OS 10.6
   0. MODELLER software ͸ɺ
   λϯύΫ࣭ͷϗϞϩδʔϞσϦϯάΛߏங͢ΔͨΊͷίϯϐϡ
   ʔλϓϩάϥϜ (Academic Free) Ͱ͋ΔɻຊϓϩάϥϜ͸ɺThe University of California, San
   Francisco (UCSF)ͷ Abdrej Sali ത࢜ΒʹΑΓఏڙ͞Ε͍ͯΔ[1]ɻ
   ະ஌λϯύΫ࣭ͷߏ଄༧ଌ
   (ϗϞϩδʔϞσϦϯά)ɺಛఆͷΞϛϊࢎ࢒ج΁ͷมҟಋೖɺϖϓνυλάಋೖ࣌΍༥߹
   λϯύΫ࣭ͷߏ଄༧ଌͳͲඇৗʹ൚༻ੑ͕ߴ͍ɻ
   1. ·ͣɺMODELLER Λμ΢ϯϩʔυ & Πϯετʔϧ͢Δɻ
   (http://salilab.org/modeller/download_installation.html)
   2. Protein Data Bank (http://www.rcsb.org/pdb/home/home.do)ΑΓɺ
   Template ͱͯ͠༻͍Δλϯ
   ύΫ࣭ͷߏ଄ϑΝΠϧ(PDB ܗࣜ)Λμ΢ϯϩʔυ͢Δɻ͜ͷ৔߹͸ɺPDB ID = 2CZT Λμ΢
   ϯϩʔυͨ͠ɻ
   3. ali ϑΝΠϧͷ࡞੡
   ςΩετͰҎԼͷจࣈྻΛ࡞੡͢Δɻ
   ϑΝΠϧ໊: unknownStructure.ali
   ***********************************************
   >P1;unknownStructure # Ϟσϧߏ଄ͷγʔΫΤϯε
   sequence:unknownStructure:::::::: # จ຤ʹ : (ίϩϯ)Λ 8 ݸهड़
   FQQDKFLGRWFSAGLASNSSWLREKKAALSMAKSVVAPATDGGLNLTSTFLRK
   NQCETRTMLLQPAGSLGSYSYRSPHWGSTYSVSVVETDYDQYALLYSQGSKGP
   GEDFRMATLYSRTQTPRAELKEKFTAFAKAQGFTEDTIVFLPQTDKCMTE*
   >P1;2CZT # ςϯϓϨʔτͷγʔΫΤϯε
   structureX:2CZT:FIRST:A:LAST:A:::: # Chain A Λ࢖༻
   FQQDKFLGRWYSAGLASNSSWFREKKAVLYMAKTVVAPSTEGGLNLTSTFLRK
   N-CETKIMVLQPAGAPGHYTYSSPHSGSIHSVSVVEANYDEYALLFSRGTKGP
   GQDFRMATLYSRTQTLKDELKEKFTTFSKAQGLTEEDIVFLPQPDKCIQE*
   ***********************************************
   ˞ unknownStructure ͷΞϛϊࢎ࢒ج਺͸ɺςϯϓϨʔτͱಉ͡ʹ͢Δɻ
   ˞ PDB ϑΝΠϧͱ structureX ͷΞϥΠϯϝϯτΛશ͘ಉ͡ʹ͢Δɻ
   ཱମߏ଄͕ղ͔Ε͍ͯ
   ͳ͍෦෼͸ɺద࣌”- (ϋΠϑϯ)”ΛೖΕΔɻ
   ˞ vi ίϚϯυʹΑΓɺali ϑΝΠϧΛ࡞੡͢Δ͜ͱΛਪ঑͢Δɻ
   

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2. 2
   4. py ϑΝΠϧͷ࡞੡
   ςΩετͰҎԼͷจࣈྻΛ࡞੡͢Δɻ
   ϑΝΠϧ໊: modeller.py
   ***********************************************
   #!/usr/bin/python
   from modeller import *
   from modeller.automodel import *
   env = environ()
   a = automodel(
   env,
   alnfile = 'unknownStructure.ali', # ali ͷϑΝΠϧ໊
   knowns = '2CZT', # ςϯϓϨʔτͷγʔΫΤϯε໊
   sequence = 'unknownStructure', # Ϟσϧߏ଄ͷγʔΫΤϯε໊
   assess_methods = (assess.D OPE, assess.GA341),
   )
   a.starting_model = 1
   a.ending_model = 50 # ܭࢉճ਺ ͜ͷ৔߹ɺ50 ݸͷϞσϧߏ଄Λ࡞੡͢Δ
   a.make()
   ***********************************************
   ˞ ඞ֦ͣுࢠΛ.py ʹมߋ͢Δɻ
   ˞ vi ίϚϯυʹΑΓɺpy ϑΝΠϧΛ࡞੡͢Δ͜ͱΛਪ঑͢Δɻ
   ˞ PDBɺaliɺ͓Αͼ py ϑΝΠϧΛಉ͡࡞ۀϑΥϧμʹஔ͘ɻ
   5. λʔϛφϧΛىಈɻ্هͷ࡞ۀϑΥϧμʹҠಈ͢Δɻ
   6. MODELLER ʹΑΔϞσϧߏ଄ܭࢉ
   (࡞ۀϑΥϧμ಺) % mod9v7 modeller.py
   ্هʹΑΓɺMODELLER ͕࣮ߦ͞ΕΔɻΤϥʔϝοηʔδ͕දࣔ͞ΕΔ৔߹͸ɺlog ϑΝ
   ΠϧΛ֬ೝ͢Δɻ
   ଟ͘ͷ৔߹ɺ
   ྆ऀؒͷΞϥΠϝϯτ͕ؒҧ͍ͬͯΔͱ͍͏ΤϥʔͰ͋Δɻ
   ˞ ݱࡏͷ࠷৽όʔδϣϯͰ͸ɺ% mod9v10 modeller.py ͱ࣮ߦ͢Δɻ
   

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3. 3
   7. ܭࢉ͞Εͨ PDB ϑΝΠϧͷߏ଄ධՁ (UCLA ͷ NIH MBI Laboratory Servers Λར༻)
   ERRAT2ʢhttp://nihserver.mbi.ucla.edu/ERRATv2/ʣ
   ˞ Overall quality factor ͕ߴ͍ߏ଄ΛબͿɻ
   ͋Δ͍͸
   SAVES; The Structure Analysis and Verification Server (http://services.mbi.ucla.edu/SAVES/)
   ˞ ERRAT ΛؚΉෳ߹తͳߏ଄ධՁαʔόʔ
   ˞ ΋ͬͱ΋είΞ͕ྑ͍Ϟσϧߏ଄Λબ୒͢Δɻ
   Reference
   [1] A. Sali & T.L. Blundell. Comparative protein modelling by satisfaction of spatial restraints. J.
   Mol. Biol. 234, 779-815, 1993.
   

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