Dear DS users and moderators,
Thank you so much for your prompt replies to my previous questions.
I am trying to build a homology model for my target protein. For this purpose, I did BLAST search (NCBI server) vs. pdbaa using DS25. Fortunately, I found ideal template protein with 83 % identity. Afterward, I did from “View Results”--> Blast Window--> Load structure and Alignment on the one template protein. Now I can see the alignment of my target with template protein sequence. I have a little bit confusion that what do I have to do further for homology model of my protein. However, I did multiple sequence alignment using “Align multiple sequences” by “Align Sequences” in “Alignment type”. Subsequently, Now I try to use the “Build Homology models” in protocol but in the parameters, I can not input anything such as Template structure, Input sequence Alignment and Input template structure. Etc.
Since there are many options, my question is that after finding good template using Blast search, what do I have to do or what are the next particular steps for building homology models??
Million thanks in advance.
Thank you so much for your prompt replies to my previous questions.
I am trying to build a homology model for my target protein. For this purpose, I did BLAST search (NCBI server) vs. pdbaa using DS25. Fortunately, I found ideal template protein with 83 % identity. Afterward, I did from “View Results”--> Blast Window--> Load structure and Alignment on the one template protein. Now I can see the alignment of my target with template protein sequence. I have a little bit confusion that what do I have to do further for homology model of my protein. However, I did multiple sequence alignment using “Align multiple sequences” by “Align Sequences” in “Alignment type”. Subsequently, Now I try to use the “Build Homology models” in protocol but in the parameters, I can not input anything such as Template structure, Input sequence Alignment and Input template structure. Etc.
Since there are many options, my question is that after finding good template using Blast search, what do I have to do or what are the next particular steps for building homology models??
Million thanks in advance.
