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:
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TEMPLATE:A|PDBID|CHAIN|SEQUENCE
ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTD
SEEEIREAFRVFDKDGNGFISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVTMMTSK
TEMPLATE:B|PDBID|CHAIN|SEQUENCE
KRRWKKNFIAVSAANRFKKISSSGAL
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the residue number of Chanin A:148; Chain B:26
The sequence of the target is as listed:
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TARGET:A|PDBID|CHAIN|SEQUENCE
ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELADMINEVDADGNGTIDFPEFLTMMARKMKDTD
SEEKIREAFRVFDKDGNGFISAKELRHVMTNLGEKLKDEEVDEMIREADIDGDGQVNYEEFVTMMTSK
TARGET:B|PDBID|CHAIN|SEQUENCE
KLRWLKNFIAVSKKNRFLKISSSGAL
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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:
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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-----------------
-------------------------------*
****************************************************************************
