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 *