Michael Tress.
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. 
Madrid-Jan-05

Practical sections of homology modelling and fold recognition

This page contains practical examples with proposed targets for:

1.-HOMOLOGY MODELLING Skip this introduction page and OPEN a new window! If there is any structural homologue to the target. See PDB blast decision table below
2.-FOLD RECOGNITION Skip this introduction page and OPEN a new window! If there is no structural homologue to the target. See PDB blast decision table

This site is a complementary guide for the theroretical part of the course. You'll find examples and useful resources regarding protein structure prediction.

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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First copy and paste your target and run BLAST at the NCBI or BLAST at the EBI against the PDB database.

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Target 1 

LSWYDPDFQARLTRSNSKCQGQLEVYLKDGWHMVCSQSWGRSSK
QWEDPSQASKVCQRLNCGVPLSLGPFLVTYTPQSSIICYGQLGS
FSNCSHSRNDMCHSLGLTCLE
 Target 2 
MTSSPTSTQESSTSWYLLLQQLIDGESLSRSQAAELMQGWLSEA
VPPELSGAILTALNFGVSADELTGMAEVLQSQSKMGTGENYSQL
PITNSPFSIIDTCGTGGDGSSTFNISTAVAVAAAYGVPVAKHGN
RSASSLTGSADVLEALGVNLGASPEKVQAALQEVGITFLFAPGW
HALKAVATLRRTLRIRTVFNLLGPLVNPLRPTGQVVGLFTPKLL
TTVAQALDNLGKQKAILHGRERLDEAGLGDLTDLAVLSDGELQL
TTINPQEVGVTPAPIGALRGGDVQENAEILKVLQGKGTQAQQDA
VALNAALALQVAGAVPLLDHAQGVSVAKEILQTGTAWAKLAQLV
YFGN
Target 3 

MLGAMAEEAVAPVAVPTTQEQPTSQPAAAQVTTVTSPSVTATAAAATAAV
ASPQANGNAASPVAPASSTSRPAEELTCMWQGCSEKLPTPESLYEHVCER
HVGRKSTNNLNLTCQWGSCRTTTVKRDHITSHIRVHVPLKPHKCDFCGKA
FKRPQDLKKHVKTHADDSVLVRSPEPGSRNPDMMFGGNGKGYAAAHYFEP
ALNPVPSQGYAHGPPQYYQAHHAPQPSNPSYGNVYYALNTGPEPHQASYE
SKKRGYDALNEFFGDLKRRQFDPNSYAAVGQRLLSLQNLSLPVLTAAPLP
EYQAMPAPVAVASGPYGGGPHPAPAYHLPPMSNVRTKNDLINIDQFLQQM
QDTIYENDDNVAAAGVAQPGAHYIHNGISYRTTHSPPTQLPSAHATTQTT
AGPIISNTSAHSPSSSTPALTPPSSAQSYTSGRSPISLPSAHRVSPPHES
GSSMYPRLPSATDGMTSGYTAASSAAPPSTLGGIFDNDERRRYTGGTLQR
ARPASRAASESMDLSSDDKESGERTPKQISASLIDPALHSGSPGEDDVTR
TAKAATEVAERSDVQSEWVEKVRLIEYLRNYIANRLERGEFSDDSEQEQD
QEQEQDQEQEQDQEQGQDRVSRSPVSKADVDMEGVERDSLPRSPRTVPIK
TDGESAEDSVMYPTLRGLDEDGDSKMPS
 Target 4 
MAGDLSAGFFMEELNTYRQKQGVVLKYQELPNSGPPHDRRFTFQVIIDG
REFPEGEGRSKKEAKNAAAKLAVEILNKEKKAVSPLLLTTTNSSEGLSM
GNYIGLINRIAQKKRLTVNYEQCASGVHGPEGFHYKCKMGQKEYSIGTG
STKQEAKQLAAKLAYLQILSEETSVKSDYLSSGSFATTCESQSNSLVTS
TLASESSSEGDFSADTSEINSNSDSLNSSSLLMNGLRNNQRKAKRSLAP
RFDLPDMKETKYTVDKRFGMDFKEIELIGSGGFGQVFKAKHRIDGKTYV
IKRVKYNNEKAEREVKALAKLDHVNIVHYNGCWDGFDYDPETSDDSLES
SDYDPENSKNSSRSKTKCLFIQMEFCDKGTLEQWIEKRRGEKLDKVLAL
ELFEQITKGVDYIHSKKLIHRDLKPSNIFLVDTKQVKIGDFGLVTSLKN
DGKRTRSKGTLRYMSPEQISSQDYGKEVDLYALGLILAELLHVCDTAFE
TSKFFTDLRDGIISDIFDKKEKTLLQKLLSKKPEDRPNTSEILRTLTVW
KSPEKNERHTC
Target 5 

MDVFMKGLSKAKEGVVAAAEKTKQGVAEAAGKTKE
GVLYVGSKTKEGVVHGVTTVAEKTKEQVTNVGGAV
VTGVTAVAQKTVEGAGNIAAATGFVKKDQMGKGEE
GYPQEGILEDMPVDPGSEAYEMPSEEGYQDYEPEA
LHPAIMLRRRGDFEEVAMMNGSDNVTPGGRL
 Target 6 

MTLFTTSATRSRRATASIVAGMTLAGAAAVGFSAPAQAAT
VDTWDRLAECESNGTWDINTGNGFYGGVQFTLSSWQAVGG
EGYPHQASKAEQIKRAEILQDLQGWGAWPLCSQKLGLTQA
DADAGDVDATEAAPVAVERTATVQRQSAADEAAAEQAAAA
EQAVVAEAETIVVKSGDSLWTLANEYEVEGGWTALYEANK
GAVSDAAVIYVGQELVLPQA

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

PDB BLAST decision table

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Does the target have <25% ID with any PDB structure?

Is the aligned length less 80% of total length of the target sequence?

Is the alignment "gappy"?

If the answer is NO If you answered YES to any question
Then Consider Homology Modelling Consider Fold Recognition