[modeller_usage]molecular modelling with multiple chains
Hello all, Could you please tell me how to perform molecular modelling with multiple chains? I get trouble in preparing the alignment file in this case.
The sequence of the template is as follows:
******************************************************************************** TEMPLATE:A|PDBID|CHAIN|SEQUENCE ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTD SEEEIREAFRVFDKDGNGFISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVTMMTSK TEMPLATE:B|PDBID|CHAIN|SEQUENCE KRRWKKNFIAVSAANRFKKISSSGAL ******************************************************************************** the residue number of Chanin A:148; Chain B:26
The sequence of the target is as listed:
******************************************************************************** TARGET:A|PDBID|CHAIN|SEQUENCE ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELADMINEVDADGNGTIDFPEFLTMMARKMKDTD SEEKIREAFRVFDKDGNGFISAKELRHVMTNLGEKLKDEEVDEMIREADIDGDGQVNYEEFVTMMTSK TARGET:B|PDBID|CHAIN|SEQUENCE KLRWLKNFIAVSKKNRFLKISSSGAL ******************************************************************************** Both the two chains have the same number of residues compared with Template.
I want to model the protein-peptide COMPLEX (NOT one by one) of TARGET:A-TARGET:B taking the TEPLATE as template structure. Could anyone please help me to know how to prepare the allignment file and paste it to me?
Best regards,
DianFan Li China 2006-03-01
ps: the typical ali file in example of MODELLER 7v7 is:
*************************************************************************** P1;5fd1 structureX:5fd1:1 : :106 : :ferredoxin:Azotobacter vinelandii: 1.90: 0.19 AFVVTDNCIKCKYTDCVEVCPVDCFYEGPNFLVIHPDECIDCALCEPECPAQAIFSEDEVPEDMQEFIQLNAELA EVWPNITEKKDPLPDAEDWDGVKGKLQHLER* P1;1fdx sequence:1fdx:1 : :54 : :ferredoxin:Peptococcus aerogenes: 2.00:-1.00 AYVINDSC--IACGACKPECPVNIIQGS--IYAIDADSCIDCGSCASVCPVGAPNPED----------------- -------------------------------* ****************************************************************************
典范 wrote: > Could you please tell me how to perform molecular modelling with > multiple chains? I get trouble in preparing the alignment file in > this case.
Modeller should have no problem modeling a multiple-chain system. Simply put the sequences of both chains in your alignment file, and use a chain break character ('/') to separate them. So your template sequence would look something like:
>P1;5fd1 structureX:5fd1:1:A:26:B:::: ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTD SEEEIREAFRVFDKDGNGFISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVTMMTSK/ KRRWKKNFIAVSAANRFKKISSSGAL*
Obviously you would change '5fd1' to the actual PDB code of your template structure, and change the starting/ending residue IDs from 1:A and 26:B if necessary.
Ben Webb, Modeller Caretaker
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典范