Ana Rojas Mendoza.
ProteinDesign Group.
Centro Nacional de Biotecnologia (C.N.B.- C.S.I.C.)
Campus Universidad Autonoma.Cantoblanco. 28049 Madrid.
Tlf: +34-91-5854570. Fax: +34-91-5854506.
e-mail: arojas@gredos.cnb.uam.es
Madrid-Feb-04

Please, find the presentation of the course HERE

PRACTICAL SECTIONS OF
HOMOLOGY MODELING/THREADING/VISUALIZATION
PAGE

This modules page contains practical examples with proposed targets to conduct assays of:

1.-HOMOLOGY MODELING Skip this and OPEN it in a new window! If there is any strcutural homolog to my template. See PDB blast decision table below
2.-THREADING Skip this and OPEN it in a new window! If there is no structural homolog to my template: reaching the fold. See PDB blast decision table
3.-VISUALIZATION Skip this and OPEN it in a new window! YOU NEED THIS TO VISUALIZE MODELS CREATED IN THE PREVIOUS POINTS

This site is a complementary guide for the theroretical part of the course. You'll find some examples and useful resources regarding the structural part of the course, mainly dealing with proteins. This is a GUIDE, it is not intended to be a tutorial or similar resource. The practical parts have been divided in several blocks.

TRAINING SECTIONS: PRELIMINARY STEPS

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1.-First BLAST (in a new window) your target sequence

2.-Second, Consult the " Blast decision table" below to decide which approach is the proper one for the following targets

target1 LSWYDPDFQARLTRSNSKCQGQLEVYLKDGWHMVCSQSWGRSSK
QWEDPSQASKVCQRLNCGVPLSLGPFLVTYTPQSSIICYGQLGS
FSNCSHSRNDMCHSLGLTCLE
Target 6
 MIDLSKTVFYTSIDIGSRYIKGLVLGKRDQEWEALAFSSVKSRG
LDEGEIKDAIAFKESVNTLLKELEEQLQKSLRSDFVISFSSVSF
EREDTVIERDFGEEKRSITLDILSEMQSEALEKLKENGKTPLHI
FSKRYLLDDERIVFNPLDMKASKIAIEYTSIVVPLKVYEMFYNF
LQDTVKSPFQLKSSLVSTAEGVLTTPEKDRGVVVVNLGYNFTGL
IAYKNGVPIKISYVPVGMKHVIKDVSAVLDTSFEESERLIITHG
NAVYNDLKEEEIQYRGLDGNTIKTTTAKKLSVIIHARLREIMSK
SKKFFREVEAKIVEEGEIGIPGGVVLTGGGAKIPRINELATEVF
KSPVRTGCYANSDRPSIINADEVANDPSFAAAFGNVFAVSENPY
EETPVKSENPLKKIFRLFKELME
target2 MWVPSMYPVKPPFISINLENFDMNTISSSLPIQEYIDSNGWIALP
ILHCWDPAAMNLIMVVQELMSLLHEPPQDQAPSLPPKPNTQLQQE
GEYSPTAPKAQVSTPKTAIASTSTTSTGI
Target 7
 MAEDGPQKQQLEMPLVLDQDLTQQMRLRVESLKQRGEKKQDGEK
LIRPAESVYRLDFIQQQKLQFDHWNVVLDKPGKVTITGTSQNWT
PDLTNLMTRQLLDPAAIFWRKEDSDAMDWNEADALEFGERLSDL
AKIRKVMYFLITFGEGVEPANLKASVVFNQL
target3 MINRTDCNENSYLEIHNNEGRDTLCFANAGTMPVAIYGVNWVES
GNNVVTLQFQRNLSDPRLETITLQKWGSWNPGHIHEILSIRIY		 Target8
 
MAGDLSAGFFMEELNTYRQKQGVVLKYQELPNSGPPHDRRFTFQVIIDG
REFPEGEGRSKKEAKNAAAKLAVEILNKEKKAVSPLLLTTTNSSEGLSM
GNYIGLINRIAQKKRLTVNYEQCASGVHGPEGFHYKCKMGQKEYSIGTG
STKQEAKQLAAKLAYLQILSEETSVKSDYLSSGSFATTCESQSNSLVTS
TLASESSSEGDFSADTSEINSNSDSLNSSSLLMNGLRNNQRKAKRSLAP
RFDLPDMKETKYTVDKRFGMDFKEIELIGSGGFGQVFKAKHRIDGKTYV
IKRVKYNNEKAEREVKALAKLDHVNIVHYNGCWDGFDYDPETSDDSLES
SDYDPENSKNSSRSKTKCLFIQMEFCDKGTLEQWIEKRRGEKLDKVLAL
ELFEQITKGVDYIHSKKLIHRDLKPSNIFLVDTKQVKIGDFGLVTSLKN
DGKRTRSKGTLRYMSPEQISSQDYGKEVDLYALGLILAELLHVCDTAFE
TSKFFTDLRDGIISDIFDKKEKTLLQKLLSKKPEDRPNTSEILRTLTVWK
KSPEKNERHTC
target4 MLGAMAEEAVAPVAVPTTQEQPTSQPAAAQVTTVTSPSVTATAAAATAAV
ASPQANGNAASPVAPASSTSRPAEELTCMWQGCSEKLPTPESLYEHVCER
HVGRKSTNNLNLTCQWGSCRTTTVKRDHITSHIRVHVPLKPHKCDFCGKA
FKRPQDLKKHVKTHADDSVLVRSPEPGSRNPDMMFGGNGKGYAAAHYFEP
ALNPVPSQGYAHGPPQYYQAHHAPQPSNPSYGNVYYALNTGPEPHQASYE
SKKRGYDALNEFFGDLKRRQFDPNSYAAVGQRLLSLQNLSLPVLTAAPLP  EYQAMPAPVAVASGPYGGGPHPAPAYHLPPMSNVRTKNDLINIDQFLQQM
QDTIYENDDNVAAAGVAQPGAHYIHNGISYRTTHSPPTQLPSAHATTQTT
AGPIISNTSAHSPSSSTPALTPPSSAQSYTSGRSPISLPSAHRVSPPHES
GSSMYPRLPSATDGMTSGYTAASSAAPPSTLGGIFDNDERRRYTGGTLQR
ARPASRAASESMDLSSDDKESGERTPKQISASLIDPALHSGSPGEDDVTR
TAKAATEVAERSDVQSEWVEKVRLIEYLRNYIANRLERGEFSDDSEQEQD
QEQEQDQEQEQDQEQGQDRVSRSPVSKADVDMEGVERDSLPRSPRTVPIK
TDGESAEDSVMYPTLRGLDEDGDSKMPS
Target9
 MAEDGPQKQQLEMPLVLDQDLTQQMRLRVESLKQRGEKKQDGEK
LIRPAESVYRLDFIQQQKLQFDHWNVVLDKPGKVTITGTSQNWT
PDLTNLMTRQLLDPAAIFWRKEDSDAMDWNEADALEFGERLSDL
AKIRKVMYFLITFGEGVEPANLKASVVFNQL
rget5 VATAKYGTPVIDGEIDEIWNTTEEIERKAVAMGSLDKNATAKVRV
LWDENYLYVLAIVKDPVLNKDNSNPWEQDSVEIFIDENNHKTGYY
EDDDAQFRVNYMNEQTFGTGGSPARFKTAVKLIEGGYIVEAAIKW
KTIKPTPNTVIGFNIQVNDANEKGQRVGIISWSDPTNNSWRDPSK
FGNLRLIK

Target10

Copy and paste your target, blast it against PDB database at :

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    USA : mirror at the USA

Europe : mirror at the EU

PDB blast decision table

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IS my target >25% ID with any protein of PDB?

YES

NO

Then

Homology modeling

Threading








































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