Im looking for a multi sequence structural alignment tool that can align main chain atoms like main chain oxygen and main chain nitrogens in a PDB file. Or even better, one that specifically aligns based on atoms positions in the protein - finding a delta oxygen from Asp equal to a main chain oxygen from a Tyr.
Does anyone know of such a tool?
Some of the enzymes I'm looking at have important main chain oxygens in places near the catalytic site and I need to screen about 2000 other proteins if they have the same oxygen modifying pKa-s of the catalytic site. But all the alignment methods I know either detect main chain alfa carbons or side chains that repeat.
You can read: Article Multiple Alignment of protein structures and sequences for VMD
and: Article MultiSeq: Unifying sequence and structure data for evolution...
Mohamed Khedawy , with all due respect I've done the analyses through these exact software packages and are the reason for me asking this question.
The software uses alpha-carbons to do structural alignment and only looks at amino acid species through their side chains.
Its an amazing software but its not the tool I need. And I need to know if the tool I need exists or I have to build it.
So specifically if a structural alignment can be made based on main chain oxygens or main chain nitrogens. Not carbons.
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