I have a question about the suggestion given in the documentations of ab initio modeling: "to increase your chance of sampling the correct topology, a diverse set of homologous sequences, preferably with sequence changes that may have a greater impact on sampling like deletions and differences in conserved positions, may also be run since a homologue may converge towards the native structure with significantly less sampling." After generating a number of decoys of these homologous sequences, it is recommended to map these decoys to the target sequence.
Does anyone have experiences in doing this?
I have tried comparative modeling method with the silent files that containing many decoys of homologs as template_silent files. But it does not work. Probably, I used wrong options. I paste the options below. If there is something wrong, please give me some suggestions:
-loops:frag_sizes 9 3 1
-loops:frag_files inputs/aatargA09_05.200_v1_3 inputs/aatargA03_05.200_v1_3 none