View source for Protein modelling

== [[단백질 구조 모델링]] 실용 안내서== <br />
<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]



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