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AutoDock, AutoLigand, MGLTools, Vina, PyRx and more.
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 Post subject: Auto doc vina
PostPosted: Thu Aug 01, 2013 7:11 pm 
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Joined: Thu Aug 01, 2013 7:07 pm
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In our lab, we are working on biochemical characterization of Plant Glucosyltransferases . Recently we started working on protein modeling and structure prediction. This work is to know which are the amino acids structurally and catalytically important for higher substrate specific nature of one of our GTs.

To start with, we used the crystal structure information of a related protein (2C1Z) to create model of our protein in its wild type form and few mutants. We did the ligand docking with these models using Auto dock Vina. When we try to analyze the results using PyRx tool, we faced a problem. When we superimposed the two docking results, the ligand docking orientation for the WT and mutants were entirely different (difference between WT and mutant a single amino acid replacement).

Our ultimate goal is to predict changes in amino acids which will lead to the shift in substrate specificity (using different class of substrates) as well as regio-specificity (adding glucose to the 7 position instead of 3 position of the acceptor substrate) of the enzyme and test those in yeast expression system.

Since protein modeling and structure prediction is new to us and we are still in learning curve. With your expertise, I request you comment to our methods, are we in right track, how to compare and analyze ligand docking results. Is there any other software and tools we can use to achieve our goal more efficiently and accurately. I appreciate if you help me in this regard.


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