Difference between revisions of "Protein modelling"

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== [[단백질 구조 모델링]] 실용 안내서==
+
== [[단백질 구조 모델링]] 실용 안내서== <br />
−
[http://biome.ngic.re.kr/ProteinModelling/]
+
<br />
 +
[http://biome.ngic.re.kr/ProteinModelling/] <br />
 +
<br />
 +
===Problem (문제정의)=== <br />
 +
* Build 3D structural models of given or interested proteins <br />
 +
** Initial input: amino acid sequence of the target protein <br />
 +
** Final output: its predicted 3D structure <br />
 +
<br />
 +
===Method===<br />
 +
&nbsp;* Find one or more structural templates of the target protein via sequence homology search against known structures (program: BLASTP or PSI-BLAST, database: PDB)<br />
 +
* Download template structures in PDB format (web server: RCSB PDB) <br />
 +
* Align the amino acid sequence of the target protein with that(those) of the template protein(s) (program: CLUSTALW, output: PIR format) <br />
 +
* Build 3D structural models based on the multiple sequence alignment and the template 3D structure(s) (program: MODELLER, input: ATM, ALI, and TOP files) <br />
 +
** manual build <br />
 +
*** manually convert file formats from PDB to ATM and PIR to ALI, respectively <br />
 +
*** write a TOP script file <br />
 +
*** run MODELLER <br />
 +
** automatic build (some PDB and PIR files are not successfully converted to correct ATM and ALI files due to amino-acid sequence mismatch) <br />
 +
*** perl script to generate ATM, ALI, and TOP files from PDB and PIR files: [[perl script for ATM|txt]], gz <br />
 +
*** 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) <br />
 +
*** run the perl script (e.g. ../bin/makeModellerInput.pl /home/user/Protein3DModelling/KCIP KCIP.pir KCIP 1QJA.pdb) <br />
 +
*** run MODELLER (e.g. mod7v7 KCIP.top) <br />
 +
<br />
 +
** example <br />
 +
*** ATM file: 5fd1.atm <br />
 +
*** ALI file: alignment.ali <br />
 +
*** TOP file: model-default.top <br />
 +
*** command: mod7v7 model-default.top <br />
 +
*** output PDB file (predicted model): 1fdx.B99990001.pdb <br />
 +
** MODELLER manual <br />
 +
*** PDF, HTML<br />
 +
<br />
 +
&nbsp;* Display and compare the 3D structures of the model and the template proteins (program: RasMol) <br />
 +
<br />
 +
=== Sample proteins (단백질 예제들)=== <br />
 +
* 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 <br />
 +
<br />
 +
=== Available Online Tool Servers === <br />
 +
# BLASTP: ## [http://www.ncbi.nlm.nih.gov/BLAST/Blast.cgi?CMD=Web&amp;LAYOUT=TwoWindows&amp;AUTO_FORMAT=Semiauto&amp;ALIGNMENTS=250&amp;ALIGNMENT_VIEW=Pairwise&amp;CDD_SEARCH=on&amp;CLIENT=web&amp;DATABASE=nr&amp;DESCRIPTIONS=500&amp;ENTREZ_QUERY=%28none%29&amp;EXPECT=10&amp;FILTER=L&amp;FORMAT_OBJECT=Alignment&amp;FORMAT_TYPE=HTML&amp;I_THRESH=0.005&amp;MATRIX_NAME=BLOSUM62&amp;NCBI_GI=on&amp;PAGE=Proteins&amp;PROGRAM=blastp&amp;SERVICE=plain&amp;SET_DEFAULTS.x=41&amp;SET_DEFAULTS.y=5&amp;SHOW_OVERVIEW=on&amp;END_OF_HTTPGET=Yes&amp;SHOW_LINKOUT=yes&amp;GET_SEQUENCE=yes 'NCBI BLASTP'] ## [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-page+Launch+-id+1uBRI1Ot9iE+-appl+BlastP+-launchFrom+top EBI SRS BLASTP] <br />
 +
<br />
 +
# PSI-BLAST: <br />
 +
## [http://www.ncbi.nlm.nih.gov/BLAST/Blast.cgi?CMD=Web&amp;LAYOUT=TwoWindows&amp;AUTO_FORMAT=Semiauto&amp;ALIGNMENTS=250&amp;ALIGNMENT_VIEW=Pairwise&amp;CLIENT=web&amp;COMPOSITION_BASED_STATISTICS=on&amp;DATABASE=nr&amp;CDD_SEARCH=on&amp;DESCRIPTIONS=500&amp;ENTREZ_QUERY=%28none%29&amp;EXPECT= 'NCBI PSI-BLAST'] <br />
 +
# CLUSTALW: <br />
 +
## [http://www.ebi.ac.uk/clustalw/ 'EBI ClustalW'], <br />
 +
## [http://www.genebee.msu.su/clustal/basic.html 'Genebee ClustalW'] # SRS servers: 'NGIC SRS', 'Public SRS servers' # Search engine: Google (Search online servers by yourself!) <br />
 +
<br />
 +
===Available Online Databases === <br />
 +
# PDB amino-acid FASTA file: NCBI BLAST DB (local: pdbaa.gz) # PDB: ## [http://www.rcsb.org/pdb/ RCSB], ## [http://pdb.ccdc.cam.ac.uk/pdb/ 'UK PDB mirror'], <br />
 +
## [http://pdb.protein.osaka-u.ac.jp/pdb/ 'Japan PDB mirror'] ===Downloadable programs=== # BLAST: ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/ (local: DOS) # CLUSTALW: ftp://ftp.ebi.ac.uk/pub/software/dos/clustalw/ (local: DOS[WindowsXP]) # MODELLER: http://salilab.org/modeller/ (local: DOS) # RasMol: http://www.openrasmol.org/ (local: Windows) # Perl: http://www.perl.org/ (local: DOS[WindowsXP]) # Other utilities: ALZip.exe (for unzip, untar, and ungzip) <br />
 +
<br />
 +
===Solution Example === <br />
 +
# Found templates (PDB format) ## Sample protein A: [http://biome.ngic.re.kr/ProteinModelling/templates/1QJA.pdb 1QJA.pdb] ## Sample protein B: [http://biome.ngic.re.kr/ProteinModelling/templates/1N4C.pdb 1N4C.pdb] -------------------------------------------------------------------------------- <br />
 +
# Multiple sequence alignments (PIR format) <br />
 +
## Sample protein A: [http://biome.ngic.re.kr/ProteinModelling/buildingModels/KCIP/modellerResult/KCIP.pir KCIP.pir] <br />
 +
## Sample protein B: [http://biome.ngic.re.kr/ProteinModelling/buildingModels/GAKH/modellerResult/GAKH.pir.ORG GAKH.pir.ORG] -------------------------------------------------------------------------------- * MODELLER input files ** Sample protein A: *** [http://biome.ngic.re.kr/ProteinModelling/buildingModels/KCIP/modellerResult/1QJA.atm ATM], *** [http://biome.ngic.re.kr/ProteinModelling/buildingModels/KCIP/modellerResult/KCIP.ali ALI], *** [http://biome.ngic.re.kr/ProteinModelling/buildingModels/KCIP/modellerResult/KCIP.top TOP] files (automatically generated) ** Sample protein B: *** [http://biome.ngic.re.kr/ProteinModelling/buildingModels/GAKH/modellerResult/1N4C.atm ATM], *** [http://biome.ngic.re.kr/ProteinModelling/buildingModels/KCIP/modellerResult/KCIP.ali ALI], *** [http://biome.ngic.re.kr/ProteinModelling/buildingModels/GAKH/modellerResult/GAKH.top TOP] files (manually edited; C-terminal only) * MODELLER output files ** Sample protein A: [http://biome.ngic.re.kr/ProteinModelling/buildingModels/KCIP/modellerResult/KCIP.pdb KCIP.pdb] ** Sample protein B: [http://biome.ngic.re.kr/ProteinModelling/buildingModels/GAKH/modellerResult/GAKH.pdb GAKH.pdb]
  
−
===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)
+
<div id="kbektt12951" style="overflow:auto;height:1px;">
−
* Align the amino acid sequence of the target protein with that(those) of the template protein(s) (program: CLUSTALW, output: PIR format)
+
[http://www.fecaltransfusionfoundation.org/anyboard9/webmaster/posts/5.html buy ambien]
−
* Build 3D structural models based on the multiple sequence alignment and the template 3D structure(s) (program: MODELLER, input: ATM, ALI, and TOP files)
+
[http://www.fecaltransfusionfoundation.org/anyboard9/webmaster/posts/6.html buy adipex]
−
** manual build
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*** manually convert file formats from PDB to ATM and PIR to ALI, respectively
+
[http://www.fecaltransfusionfoundation.org/anyboard9/webmaster/posts/8.html buy carisoprodol]
−
*** write a TOP script file
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−
*** run MODELLER
+
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** automatic build (some PDB and PIR files are not successfully converted to correct ATM and ALI files due to amino-acid sequence mismatch)
+
[http://www.appli.se/rebecca/anyboard/myboard/posts/52.html buy adipex]
−
*** perl script to generate ATM, ALI, and TOP files from PDB and PIR files: [[perl script for ATM|txt]], gz
+
[http://www.appli.se/rebecca/anyboard/myboard/posts/53.html buy xenical]
−
*** 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)
+
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−
*** run the perl script (e.g. ../bin/makeModellerInput.pl /home/user/Protein3DModelling/KCIP KCIP.pir KCIP 1QJA.pdb)
+
[http://www.appli.se/rebecca/anyboard/myboard/posts/55.html buy hydrocodone]
−
*** run MODELLER (e.g. mod7v7 KCIP.top)
+
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−
** example
+
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−
*** ATM file: 5fd1.atm
+
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−
*** ALI file: alignment.ali
+
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−
*** TOP file: model-default.top
+
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−
*** command: mod7v7 model-default.top
+
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−
*** output PDB file (predicted model): 1fdx.B99990001.pdb
+
[http://www.appli.se/rebecca/anyboard/myboard/posts/62.html download ringtones]
−
** MODELLER manual
+
[http://www.appli.se/rebecca/anyboard/myboard/posts/63.html cingular ringtones]
−
*** PDF, HTML
+
[http://www.appli.se/rebecca/anyboard/myboard/posts/64.html sprint ringtones]
−
* Display and compare the 3D structures of the model and the template proteins (program: RasMol)
+
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−
 
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=== Sample proteins (단백질 예제들)===
+
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−
* Sample protein A: 14-3-3 protein gamma (Protein kinase C inhibitor protein-1; KCIP-1)
+
[http://www.appli.se/rebecca/anyboard/myboard/posts/68.html mp3 ringtones]
−
 
+
[http://www.appli.se/rebecca/anyboard/myboard/posts/69.html cell phone ringtones]
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>sw|P61981|143G_HUMAN 14-3-3 protein gamma (Protein kinase C inhibitor protein-1) (KCIP-1)
+
[http://www.appli.se/rebecca/anyboard/myboard/posts/70.html download free ringtones]
−
VDREQLVQKARLAEQAERYDDMAAAMKNVTELNEPLSNEERNLLSVAYKNVVGARRSSWR
+
[http://www.appli.se/rebecca/anyboard/myboard/posts/71.html t-mobile ringtones]
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VISSIEQKTSADGNEKKIEMVRAYREKIEKELEAVCQDVLSLLDNYLIKNCSETQYESKV
+
[http://www.appli.se/rebecca/anyboard/myboard/posts/72.html nokia ringtones]
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FYLKMKGDYYRYLAEVATGEKRATVVESSEKAYSEAHEISKEHMQPTHPIRLGLALNYSV
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[http://www.appli.se/rebecca/anyboard/myboard/posts/73.html free cingular ringtones]
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FYYEIQNAPEQACHLAKTAFDDAIAELDTLNEDSYKDSTLIMQLLRDNLTLWTSDQQDDD
+
[http://www.appli.se/rebecca/anyboard/myboard/posts/74.html Justin Timberlake concert tickets]
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GGEGNN
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* Sample protein B: GAK_HUMAN Cyclin G-associated kinase (GAKH)
+
[http://www.appli.se/rebecca/anyboard/myboard/posts/77.html Pink concert tickets]
−
 
+
[http://www.orangefridge.com/anyboard9/ryan/posts/163.html buy ambien]
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>sw|O14976|GAK_HUMAN Cyclin G-associated kinase
+
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MSLLQSALDFLAGPGSLGGASGRDQSDFVGQTVELGELRLRVRRVLAEGGFAFVYEAQDV
+
[http://www.orangefridge.com/anyboard9/ryan/posts/165.html buy xenical]
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GSGREYALKRLLSNEEEKNRAIIQEVCFMKKLSGHPNIVQFCSAASIGKEESDTGQAEFL
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[http://www.orangefridge.com/anyboard9/ryan/posts/166.html buy carisoprodol]
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LLTELCKGQLVEFLKKMESRGPLSCDTVLKIFYQTCRAVQHMHRQKPPIIHRDLKVENLL
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LSNQGTIKLCDFGSATTISHYPDYSWSAQRRALVEEEITRNTTPMYRTPEIIDLYSNFPI
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GEKQDIWALGCILYLLCFRQHPFEDGAKLRIVNGKYSIPPHDTQYTVFHSLIRAMLQVNP
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EERLSIAEVVHQLQEIAAARNVNPKSPITELLEQNGGYGSATLSRGPPPPVGPAGSGYSG
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GLALAEYDQPYGGFLDILRGGTERLFTNLKDTSSKVIQSVANYAKGDLDISYITSRIAVM
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SFPAEGVESALKNNIEDVRLFLDSKHPGHYAVYNLSPRTYRPSRFHNRVSECGWAARRAP
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HLHTLYNICRNMHAWLRQDHKNVCVVHCMDGRAASAVAVCSFLCFCRLFSTAEAAVYMFS
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MKRCPPGIWPSHKRYIEYMCDMVAEEPITPHSKPILVRAVVMTPVPLFSKQRSGCRPFCE
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VYVGDERVASTSQEYDKMRDFKIEDGKAVIPLGVTVQGDVLIVIYHARSTLGGRLQAKMA
+
[http://www.orangefridge.com/anyboard9/ryan/posts/175.html cingular ringtones]
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SMKMFQIQFHTGFVPRNATTVKFAKYDLDACDIQEKYPDLFQVNLEVEVEPRDRPSREAP
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[http://www.orangefridge.com/anyboard9/ryan/posts/176.html sprint ringtones]
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PWENSSMRGLNPKILFSSREEQQDILSKFGKPELPRQPGSTAQYDAGAGSPEAEPTDSDS
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PPSSSADASRFLHTLDWQEEKEAETGAENASSKESESALMEDRDESEVSDEGGSPISSEG
+
[http://www.ohiospice.com/forum1/posts/11971.html buy ambien]
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QEPRADPEPPGLAAGLVQQDLVFEVETPAVLPEPVPQEDGVDLLGLHSEVGAGPAVPPQA
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CKAPSSNTDLLSCLLGPPEAASQGPPEDLLSEDPLLLASPAPPLSVQSTPRGGPPAAADP
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FGPLLPSSGNNSQPCSNPDLFGEFLNSDSVTVPPSFPSAHSAPPPSCSADFLHLGDLPGE
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PSKMTASSSNPDLLGGWAAWTETAASAVAPTPATEGPLFSPGGQPAPCGSQASWTKSQNP
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DPFADLGDLSSGLQGSPAGFPPGGFIPKTATTPKGSSSWQTSRPPAQGASWPPQAKPPPK
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ACTQPRPNYASNFSVIGAREERGVRAPSFAQKPKVSENDFEDLLSNQGFSSRSDKKGPKT
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IAEMRKQDLAKDTDPLKLKLLDWIEGKERNIRALLSTLHTVLWDGESRWTPVGMADLVAP
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EQVKKHYRRAVLAVHPDKAAGQPYEQHAKMIFMELNDAWSEFENQGSRPLF
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=== Available Online Tool Servers ===
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−
# BLASTP:
+
[http://fudan7819.phm.utoronto.ca/fudan7819/posts/2273.html verizon ringtones]
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## [http://www.ncbi.nlm.nih.gov/BLAST/Blast.cgi?CMD=Web&LAYOUT=TwoWindows&AUTO_FORMAT=Semiauto&ALIGNMENTS=250&ALIGNMENT_VIEW=Pairwise&CDD_SEARCH=on&CLIENT=web&DATABASE=nr&DESCRIPTIONS=500&ENTREZ_QUERY=%28none%29&EXPECT=10&FILTER=L&FORMAT_OBJECT=Alignment&FORMAT_TYPE=HTML&I_THRESH=0.005&MATRIX_NAME=BLOSUM62&NCBI_GI=on&PAGE=Proteins&PROGRAM=blastp&SERVICE=plain&SET_DEFAULTS.x=41&SET_DEFAULTS.y=5&SHOW_OVERVIEW=on&END_OF_HTTPGET=Yes&SHOW_LINKOUT=yes&GET_SEQUENCE=yes 'NCBI BLASTP']
+
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## [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-page+Launch+-id+1uBRI1Ot9iE+-appl+BlastP+-launchFrom+top EBI SRS BLASTP]  
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# PSI-BLAST:
+
[http://fudan7819.phm.utoronto.ca/fudan7819/posts/2276.html download ringtones]
−
## [http://www.ncbi.nlm.nih.gov/BLAST/Blast.cgi?CMD=Web&LAYOUT=TwoWindows&AUTO_FORMAT=Semiauto&ALIGNMENTS=250&ALIGNMENT_VIEW=Pairwise&CLIENT=web&COMPOSITION_BASED_STATISTICS=on&DATABASE=nr&CDD_SEARCH=on&DESCRIPTIONS=500&ENTREZ_QUERY=%28none%29&EXPECT= 'NCBI PSI-BLAST']  
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# CLUSTALW:
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[http://fudan7819.phm.utoronto.ca/fudan7819/posts/2278.html sprint ringtones]
−
## [http://www.ebi.ac.uk/clustalw/ 'EBI ClustalW'],
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## [http://www.genebee.msu.su/clustal/basic.html 'Genebee ClustalW']  
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# SRS servers: 'NGIC SRS', 'Public SRS servers'
+
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# Search engine: Google (Search online servers by yourself!)
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[http://fudan7819.phm.utoronto.ca/fudan7819/posts/2283.html cell phone ringtones]
−
===Available Online Databases ===
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# PDB amino-acid FASTA file: NCBI BLAST DB (local: pdbaa.gz)
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[http://fudan7819.phm.utoronto.ca/fudan7819/posts/2285.html t-mobile ringtones]
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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']  
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===Downloadable programs===
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# BLAST: ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/ (local: DOS)
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# CLUSTALW: ftp://ftp.ebi.ac.uk/pub/software/dos/clustalw/ (local: DOS[WindowsXP])
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# MODELLER: http://salilab.org/modeller/ (local: DOS)
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# RasMol: http://www.openrasmol.org/ (local: Windows)
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# Perl: http://www.perl.org/ (local: DOS[WindowsXP])
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# Other utilities: ALZip.exe (for unzip, untar, and ungzip)
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[http://www.ohiospice.com/forum1/posts/11989.html sprint ringtones]
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===Solution Example  ===
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# Found templates (PDB format)
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## Sample protein A: [http://biome.ngic.re.kr/ProteinModelling/templates/1QJA.pdb 1QJA.pdb]  
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## Sample protein B: [http://biome.ngic.re.kr/ProteinModelling/templates/1N4C.pdb 1N4C.pdb]  
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--------------------------------------------------------------------------------
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# Multiple sequence alignments (PIR format)
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## Sample protein A: [http://biome.ngic.re.kr/ProteinModelling/buildingModels/KCIP/modellerResult/KCIP.pir KCIP.pir]  
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## Sample protein B: [http://biome.ngic.re.kr/ProteinModelling/buildingModels/GAKH/modellerResult/GAKH.pir.ORG GAKH.pir.ORG]  
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--------------------------------------------------------------------------------
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* MODELLER input files
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** Sample protein A:
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*** [http://biome.ngic.re.kr/ProteinModelling/buildingModels/KCIP/modellerResult/1QJA.atm ATM],
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*** [http://biome.ngic.re.kr/ProteinModelling/buildingModels/KCIP/modellerResult/KCIP.ali ALI],
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*** [http://biome.ngic.re.kr/ProteinModelling/buildingModels/KCIP/modellerResult/KCIP.top TOP] files (automatically generated)
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** Sample protein B:
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*** [http://biome.ngic.re.kr/ProteinModelling/buildingModels/GAKH/modellerResult/1N4C.atm ATM],
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*** [http://biome.ngic.re.kr/ProteinModelling/buildingModels/KCIP/modellerResult/KCIP.ali ALI],
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*** [http://biome.ngic.re.kr/ProteinModelling/buildingModels/GAKH/modellerResult/GAKH.top TOP] files (manually edited; C-terminal only)
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* MODELLER output files
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** Sample protein A: [http://biome.ngic.re.kr/ProteinModelling/buildingModels/KCIP/modellerResult/KCIP.pdb KCIP.pdb]  
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** Sample protein B: [http://biome.ngic.re.kr/ProteinModelling/buildingModels/GAKH/modellerResult/GAKH.pdb GAKH.pdb]
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</div>

Latest revision as of 16:01, 30 March 2011

== 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: ## 'NCBI BLASTP' ## EBI SRS BLASTP


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


===Available Online Databases ===

  1. PDB amino-acid FASTA file: NCBI BLAST DB (local: pdbaa.gz) # PDB: ## RCSB, ## 'UK PDB mirror',
    1. 'Japan PDB mirror' ===Downloadable programs=== # BLAST: ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/ (local: DOS) # CLUSTALW: ftp://ftp.ebi.ac.uk/pub/software/dos/clustalw/ (local: DOS[WindowsXP]) # MODELLER: http://salilab.org/modeller/ (local: DOS) # RasMol: http://www.openrasmol.org/ (local: Windows) # Perl: http://www.perl.org/ (local: DOS[WindowsXP]) # Other utilities: ALZip.exe (for unzip, untar, and ungzip)


===Solution Example ===

  1. Found templates (PDB format) ## Sample protein A: 1QJA.pdb ## Sample protein B: 1N4C.pdb --------------------------------------------------------------------------------
  2. 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) * MODELLER output files ** Sample protein A: KCIP.pdb ** Sample protein B: GAKH.pdb


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