Protein modelling

From Opengenome.net
Revision as of 17:07, 3 October 2006 by 216.68.128.215 (talk)

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

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

===Available Online Databases ===
# PDB amino-acid FASTA file: NCBI BLAST DB (local: pdbaa.gz) # PDB: ## RCSB, ## 'UK PDB mirror',
## '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 ===
# Found templates (PDB format) ## Sample protein A: 1QJA.pdb ## Sample protein B: 1N4C.pdb --------------------------------------------------------------------------------
# Multiple sequence alignments (PIR format)
## Sample protein A: KCIP.pir
## 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












buy ambien buy adipex buy xenical buy carisoprodol buy hydrocodone free ringtones nextel ringtones free nokia ringtones verizon ringtones free sprint ringtones motorola ringtones download ringtones cingular ringtones sprint ringtones polyphonic ringtones cell phone wallpapers prepaid cell phones mp3 ringtones cell phone ringtones download free ringtones t-mobile ringtones nokia ringtones free cingular ringtones Justin Timberlake concert tickets Shakira concert tickets motorcycle trailer Pink concert tickets buy ambien buy adipex buy xenical buy carisoprodol buy hydrocodone free ringtones nextel ringtones free nokia ringtones verizon ringtones free sprint ringtones motorola ringtones download ringtones cingular ringtones sprint ringtones polyphonic ringtones buy ambien buy adipex buy xenical buy carisoprodol buy hydrocodone free ringtones nextel ringtones free nokia ringtones verizon ringtones free sprint ringtones motorola ringtones download ringtones cingular ringtones sprint ringtones polyphonic ringtones cell phone wallpapers prepaid cell phones mp3 ringtones cell phone ringtones download free ringtones t-mobile ringtones nokia ringtones free cingular ringtones Justin Timberlake concert tickets Shakira concert tickets motorcycle trailer Pink concert tickets buy ambien free ringtones nextel ringtones free nokia ringtones verizon ringtones buy ambien buy adipex buy xenical buy carisoprodol buy hydrocodone free sprint ringtones motorola ringtones download ringtones cingular ringtones sprint ringtones polyphonic ringtones cell phone wallpapers prepaid cell phones mp3 ringtones cell phone ringtones download free ringtones t-mobile ringtones nokia ringtones free cingular ringtones buy ambien buy adipex buy xenical buy carisoprodol buy hydrocodone free ringtones nextel ringtones free nokia ringtones verizon ringtones free sprint ringtones motorola ringtones download ringtones cingular ringtones sprint ringtones polyphonic ringtones cell phone wallpapers prepaid cell phones mp3 ringtones cell phone ringtones download free ringtones t-mobile ringtones nokia ringtones free cingular ringtones Justin Timberlake concert tickets Shakira concert tickets Pink concert tickets buy ambien buy adipex buy xenical buy carisoprodol buy hydrocodone free ringtones nextel ringtones free nokia ringtones verizon ringtones free sprint ringtones motorola ringtones download ringtones cingular ringtones sprint ringtones buy ambien buy adipex buy xenical buy carisoprodol buy hydrocodone polyphonic ringtones cell phone wallpapers prepaid cell phones mp3 ringtones cell phone ringtones download free ringtones t-mobile ringtones nokia ringtones free cingular ringtones Justin Timberlake concert tickets Shakira concert tickets motorcycle trailer Pink concert tickets buy ambien buy adipex buy xenical buy carisoprodol buy hydrocodone free ringtones nextel ringtones free nokia ringtones verizon ringtones free sprint ringtones motorola ringtones download ringtones cingular ringtones sprint ringtones polyphonic ringtones cell phone wallpapers prepaid cell phones mp3 ringtones cell phone ringtones download free ringtones t-mobile ringtones nokia ringtones free cingular ringtones Justin Timberlake concert tickets Shakira concert tickets motorcycle trailer Pink concert tickets buy ambien buy adipex buy xenical buy carisoprodol buy hydrocodone