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
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
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.