Difference between revisions of "Protein modelling"

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===Available Online Databases ===
 
===Available Online Databases ===
 
# PDB amino-acid FASTA file: NCBI BLAST DB (local: pdbaa.gz)  
 
# PDB amino-acid FASTA file: NCBI BLAST DB (local: pdbaa.gz)  
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# PDB: RCSB, 'UK PDB mirror', 'Japan PDB mirror'  
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# PDB:  
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## [http://www.rcsb.org/pdb/ RCSB],  
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## [http://pdb.ccdc.cam.ac.uk/pdb/ 'UK PDB mirror'],  
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## [http://pdb.protein.osaka-u.ac.jp/pdb/ 'Japan PDB mirror']
  
 
===Downloadable programs===
 
===Downloadable programs===

Revision as of 09:54, 26 August 2005

단백질 구조 모델링 실용 안내서

[1]

Problem (문제정의)

  • Build 3D structural models of given or interested proteins
    • Initial input: amino acid sequence of the target protein
    • Final output: its predicted 3D structure

Method

  • Find one or more structural templates of the target protein via sequence homology search against known structures (program: BLASTP or PSI-BLAST, database: PDB)
  • Download template structures in PDB format (web server: RCSB PDB)
  • Align the amino acid sequence of the target protein with that(those) of the template protein(s) (program: CLUSTALW, output: PIR format)
  • Build 3D structural models based on the multiple sequence alignment and the template 3D structure(s) (program: MODELLER, input: ATM, ALI, and TOP files)
    • manual build
      • manually convert file formats from PDB to ATM and PIR to ALI, respectively
      • write a TOP script file
      • run MODELLER
    • automatic build (some PDB and PIR files are not successfully converted to correct ATM and ALI files due to amino-acid sequence mismatch)
      • perl script to generate ATM, ALI, and TOP files from PDB and PIR files: txt, gz
      • command-line arguments in order: base_directory_path pir_file_name target_protein_id(exactly 4 letters) one_or_more_PDB_file_names(exactly 4-letter prefix)
      • run the perl script (e.g. ../bin/makeModellerInput.pl /home/user/Protein3DModelling/KCIP KCIP.pir KCIP 1QJA.pdb)
      • run MODELLER (e.g. mod7v7 KCIP.top)
    • example
      • ATM file: 5fd1.atm
      • ALI file: alignment.ali
      • TOP file: model-default.top
      • command: mod7v7 model-default.top
      • output PDB file (predicted model): 1fdx.B99990001.pdb
    • MODELLER manual
      • PDF, HTML
  • Display and compare the 3D structures of the model and the template proteins (program: RasMol)

Sample proteins (단백질 예제들)

  • Sample protein A: 14-3-3 protein gamma (Protein kinase C inhibitor protein-1; KCIP-1)

>sw|P61981|143G_HUMAN 14-3-3 protein gamma (Protein kinase C inhibitor protein-1) (KCIP-1) VDREQLVQKARLAEQAERYDDMAAAMKNVTELNEPLSNEERNLLSVAYKNVVGARRSSWR VISSIEQKTSADGNEKKIEMVRAYREKIEKELEAVCQDVLSLLDNYLIKNCSETQYESKV FYLKMKGDYYRYLAEVATGEKRATVVESSEKAYSEAHEISKEHMQPTHPIRLGLALNYSV FYYEIQNAPEQACHLAKTAFDDAIAELDTLNEDSYKDSTLIMQLLRDNLTLWTSDQQDDD GGEGNN

  • Sample protein B: GAK_HUMAN Cyclin G-associated kinase (GAKH)

>sw|O14976|GAK_HUMAN Cyclin G-associated kinase MSLLQSALDFLAGPGSLGGASGRDQSDFVGQTVELGELRLRVRRVLAEGGFAFVYEAQDV GSGREYALKRLLSNEEEKNRAIIQEVCFMKKLSGHPNIVQFCSAASIGKEESDTGQAEFL LLTELCKGQLVEFLKKMESRGPLSCDTVLKIFYQTCRAVQHMHRQKPPIIHRDLKVENLL LSNQGTIKLCDFGSATTISHYPDYSWSAQRRALVEEEITRNTTPMYRTPEIIDLYSNFPI GEKQDIWALGCILYLLCFRQHPFEDGAKLRIVNGKYSIPPHDTQYTVFHSLIRAMLQVNP EERLSIAEVVHQLQEIAAARNVNPKSPITELLEQNGGYGSATLSRGPPPPVGPAGSGYSG GLALAEYDQPYGGFLDILRGGTERLFTNLKDTSSKVIQSVANYAKGDLDISYITSRIAVM SFPAEGVESALKNNIEDVRLFLDSKHPGHYAVYNLSPRTYRPSRFHNRVSECGWAARRAP HLHTLYNICRNMHAWLRQDHKNVCVVHCMDGRAASAVAVCSFLCFCRLFSTAEAAVYMFS MKRCPPGIWPSHKRYIEYMCDMVAEEPITPHSKPILVRAVVMTPVPLFSKQRSGCRPFCE VYVGDERVASTSQEYDKMRDFKIEDGKAVIPLGVTVQGDVLIVIYHARSTLGGRLQAKMA SMKMFQIQFHTGFVPRNATTVKFAKYDLDACDIQEKYPDLFQVNLEVEVEPRDRPSREAP PWENSSMRGLNPKILFSSREEQQDILSKFGKPELPRQPGSTAQYDAGAGSPEAEPTDSDS PPSSSADASRFLHTLDWQEEKEAETGAENASSKESESALMEDRDESEVSDEGGSPISSEG QEPRADPEPPGLAAGLVQQDLVFEVETPAVLPEPVPQEDGVDLLGLHSEVGAGPAVPPQA CKAPSSNTDLLSCLLGPPEAASQGPPEDLLSEDPLLLASPAPPLSVQSTPRGGPPAAADP FGPLLPSSGNNSQPCSNPDLFGEFLNSDSVTVPPSFPSAHSAPPPSCSADFLHLGDLPGE PSKMTASSSNPDLLGGWAAWTETAASAVAPTPATEGPLFSPGGQPAPCGSQASWTKSQNP DPFADLGDLSSGLQGSPAGFPPGGFIPKTATTPKGSSSWQTSRPPAQGASWPPQAKPPPK ACTQPRPNYASNFSVIGAREERGVRAPSFAQKPKVSENDFEDLLSNQGFSSRSDKKGPKT IAEMRKQDLAKDTDPLKLKLLDWIEGKERNIRALLSTLHTVLWDGESRWTPVGMADLVAP EQVKKHYRRAVLAVHPDKAAGQPYEQHAKMIFMELNDAWSEFENQGSRPLF

Available Online Tool Servers

  1. BLASTP:
    1. 'NCBI BLASTP'
    2. EBI SRS BLASTP
  2. PSI-BLAST:
    1. 'NCBI PSI-BLAST'
  3. CLUSTALW:
    1. 'EBI ClustalW',
    2. 'Genebee ClustalW'
  4. SRS servers: 'NGIC SRS', 'Public SRS servers'
  5. Search engine: Google (Search online servers by yourself!)

Available Online Databases

  1. PDB amino-acid FASTA file: NCBI BLAST DB (local: pdbaa.gz)
  2. PDB:
    1. RCSB,
    2. 'UK PDB mirror',
    3. 'Japan PDB mirror'

Downloadable programs

  1. BLAST: ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/ (local: DOS)
  2. CLUSTALW: ftp://ftp.ebi.ac.uk/pub/software/dos/clustalw/ (local: DOS[WindowsXP])
  3. MODELLER: http://salilab.org/modeller/ (local: DOS)
  4. RasMol: http://www.openrasmol.org/ (local: Windows)
  5. Perl: http://www.perl.org/ (local: DOS[WindowsXP])
  6. Other utilities: ALZip.exe (for unzip, untar, and ungzip)

Solution Example

  1. Found templates (PDB format)
    1. Sample protein A: 1QJA.pdb
    2. Sample protein B: 1N4C.pdb
  1. Multiple sequence alignments (PIR format)
    1. Sample protein A: KCIP.pir
    2. Sample protein B: GAKH.pir.ORG
  • MODELLER input files
    • Sample protein A:
      • ATM,
      • ALI,
      • TOP files (automatically generated)
    • Sample protein B:
      • ATM,
      • ALI,
      • TOP files (manually edited; C-terminal only)
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