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Automated alignment and comparative modeling

Automated alignment and comparative modeling requires only the target sequence and the coordinates of the templates. The structural alignment of the known 3D structures and their alignment with the target sequence are derived automatically. However, the single most important factor that determines the quality of a model is the quality of the alignment. If the alignment is incorrect, the model will also be incorrect. For this reason, automated alignment for comparative modeling should not be used unless the sequences are so similar that the calculated alignment is likely to be correct, which usually requires more than 50% sequence identity. Instead, the alignment should be carefully inspected, optimized by hand, and checked by the CHECK_ALIGNMENT command before used in modeling. Moreover, several iterations of alignment and modeling may be necessary in general.

The sample input files for automated alignment and comparative modeling are located in directory
examples/align-model-steps. The sample TOP file is


# A sample TOP file for fully automated comparative modeling

INCLUDE                                       # include MODELLER routines
SET ATOM_FILES_DIRECTORY = './:../atom_files' # directory with input atom files
SET SEGFILE     = 'alignment.seg'             # input file w/ templates and target
SET KNOWNS      = '5fd1' '1fdn' '1fxd' '2fxb' # templates' PDB codes
SET SEQUENCE    = '1fdx'                      # target code
SET OUTPUT_CONTROL = 1 1 1 1 2
CALL ROUTINE    = 'full_homol'                # get alignment and a model



The alignment.seg file is


>P1;1fdx
structureX:1fdx:FIRST:@:54:@:ferredoxin:Peptococcus aerogenes: 2.00:-1.00
AYVINDSCIACGACKPECPVNIIQGSIYAIDADSCIDCGSCASVCPVGAPNPED*
>P1;1fdn
structureX:1fdn:FIRST:@:55:@:ferredoxin:Clostrodium acidiurici: 1.84:-1.0
*
>P1;5fd1
structureX:5fd1:FIRST:@:60:@:ferredoxin:Azotobacter vinelandii: 1.90:0.192
*
>P1;1fxd
structureX:1fxd:FIRST:@:58:@:ferredoxin:Desolfovibrio gigas: 1.70:-1.0
*
>P1;2fxb
structureX:2fxb:FIRST:@:60:@:ferredoxin:Bacillus thermoproteolyticus: 2.30:-1.0
*


next up previous contents index
Next: Frequently asked questions (FAQ) Up: Tutorial on using MODELLER Previous: Running MODELLER   Contents   Index
Ben Webb 2004-10-04