[modeller_usage] Adding ligand in protein will solve sidechain confromatin problem?
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Subject: [modeller_usage] Adding ligand in protein will solve sidechain confromatin problem?
From: Nataraj Balkrishnan <>
Date: Mon, 29 Mar 2004 19:11:10 +0100 (BST)
Dear Modeller, I modelled a protein from low identies template,and more I am having the idea of location of active site for my modelled protien for particular ligands. Since I know the active site of the model, I want to construct the sidechain of aminoacids involved in that active site,by adding ligand in that particular location.(Since I belive that the configuration of sidechain in the state of interaction with ligand would be the actual conformation of the sidechains of active site).
Now my questions are 1)Wheather my this idea is theoreticaly correct ?
2)if the answer for my question 1 is correct, what is the way or routine which I can use it for adding my ligand(small molecule,eg.,DDT) to my model?