Michael Tress
Protein Design 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-May-05

Practical Template-Based Modelling
includes homology modelling, fold recognition and visualisation

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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1.-First choose one of the target sequences in the list and run BLAST against the PDB database from one of the two links below

BLAST BLAST Server in the EU (just)

 


>Rpf (resuscitation-promoting factor)
MTLFTTSATRSRRATASIVAGMTLAGAAAVGFSAPAQAATVDTWDRLAECESNGTWDINTGNGFYGGVQFTLSSWQAVGGEGYPHQAS
KAEQIKRAEILQDLQGWGAWPLCSQKLGLTQADADAGDVDATEAAPVAVERTATVQRQSAADEAAAEQAAAAEQAVVAEAETIVVKSG
DSLWTLANEYEVEGGWTALYEANKGAVSDAAVIYVGQELVLPQA

>sir1
STEEEYVSPRFLVADGFLIDLAEEKPINPKDPRLLTLLKDHQRAMIDQMNLVKWNDFKKYQDPIPLKAKTLFKFCKQIKKKFLRGADF
KLHTLPTEANLKYEPERMTVLCSCVPILLDDQTVQYLYDD

>sir3
MAKTLKDLDGWQVIITDDQGRVIDDNNRRRSRKRGGENVFLKRISDGLSFGKGESVIFNDNVTETYSVYLIHEIRLNTLNNVVEIWVF
SYLRWFELKPKLYYEQFRPDLIKEDHPLEFYKDKFFNEVNKSELYLTAELSEIWLKDFIAVGQILPESQWNDSSIDKIEDRDFLVRYA
CEPTAEKFVPIDIFQIIRRVKEMEPKQSDEYLKRVSVPVSGQKTNR

>atu
MEDGMNTFDLYYWPVPFRGQLIRGILAHCGCSWDEHDVDAIEGLMDCGAEKQPVAFMGPPVLIDRERNFAISQMPAIAIYLGERLDIL
PATVEGRTLSAKIVNDANDVLDELTLNGGREMWTPEKWQEFVPRLQKWIRIFADTGARNGLSAASGFMLGTEKIGVADIVTAILWTTV
ADRFPAIKGIIEDTSPIIWGLSRRVVATAPLAALNSKSFEEYGNAYCGGEIEKSLRKVAS

>RPE_YEAST
MVKPIIAPSILASDFANLGCECHKVINAGADWLHIDVMDGHFVPNITLGQPIVTSLRRSVPRPGDASNTEKKPTAFFDCHMMVENPEK
WVDDFAKCGADQFTFHYEATQDPLHLVKLIKSKGIKAACAIKPGTSVDVLFELAPHLDMALVMTVEPGFGGQKFMEDMMPKVETLRAK
FPHLNIQVDGGLGKETIPKAAKAGANVIVAGTSVFTAADPHDVISFMKEEVSKELRSRDLLD

>F93
MKIRKYMRINYYIILKVLVINGSRLEKKRLRSEILKRFDIDISDGVLYPLIDSLIDDKILREEEAPDGKVLFLTEKGMKEFEELHEFF
KKIVC

>BclA
MAFDPNLVGPTLPPIPPFTLPTGPTGPTGPTGPTGPTGPTGPTGDTGTTGPTGPTGPTGPTGPTGATGLTGPTGPTGPSGLGLPAGLY
AFNSGGISLDLGINDPVPFNTVGSQFGTAISQLDADTFVISETGFYKITVIANTATASVLGGLTIQVNGVPVPGTGSSLISLGAPIVI
QAITQITTTPSLVEVIVTGLGLSLALGTSASIIIEKVAHHHHHH

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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Can you find a PDB structure with an e-value of less than 0.01?

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

Is the aligned length more than 80% of total length of the target sequence?

Are there few gaps in the alignment?

If the answer is YES to all If you answered NO to any question
Then Consider Homology modelling (opens in a new window) More work is needed. Go to Template-based Modelling (opens in a new window)


3.-VISUALISATION Skip this introduction page and OPEN a new window! If you want to visualise the models you have created