I am building protein structures for a list of query proteins via homology modelling using Modeller. In some cases the template is a homomeric protein and in others its a heteromeric protein. Could anyone please suggest how should the alignment file (containing PIR formats of target and template) look like in case of both the types of proteins. I am new to Modeller and would really appreciate the guidance.
https://salilab.org/modeller/manual/node29.html
MODELLER can build models of multi-chain proteins in exactly the same way as single-chain models; simply add one or more chain break ('/') characters to your alignment file in the appropriate locations.
I usually prefer to build single-chain alignments (using Clustal for example) and then combine them into multi-chain alignments for Modeller. This way you get better control of the results. For homomeric proteins it is just a matter of simple copy-and-paste followed by adding "chain break" (/) and "sequence end" (*) markers in the proper places. For heteromers you would need to be a bit more careful ))
Note that even the nominally identical chains in a multi-chain template PDB can sometimes have slightly different sequences for various reasons.
Also, you of course will have to know how the target protein is structured and which chains you actually need. In the simplest case, if a target is monomeric, you can just extract one chain from the template (the PDBs often may contain 2 or more copies of a protein due to crystallographic packing and/or loose association between them).
Thank you for the suggestion. I did add the '/' in case of multichain proteins and was able to align. However I also have a doubt about ligands associated with one of the chains. In my template there are two chains A & B but protein chain A has the ligands of interest. How should I depict the ligands in my multichain protein template?
I am giving a sample case
>P1,1abc
structureX::::::::
mshhtydtfthfdshsdxxxx/mtyh
mynmirthxxx*
Should I add the hetatms after chain B and if so how should it be depicted?.
I would really appreciate guidance on this point.
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