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 Post subject: Protein Conformation
PostPosted: Thu Jan 29, 2009 3:16 am 

Joined: Wed Oct 29, 2008 2:24 pm
Posts: 17
Is there a way to predict the effect a bound ligand has on the conformation of a protein. Or a way to set it up to see that.


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 Post subject: Re: Protein Conformation
PostPosted: Thu Jan 29, 2009 10:15 am 

Joined: Wed Oct 29, 2008 2:24 pm
Posts: 40
With the help of molecular dynamics, multiple conformation of the protein can be produced and used for docking calculation in Docking Server and the results then can be compared. Moreover, Autodock 4.0 has a feature "flexible docking", where certain amino acid residues can be treated as flexible- but this feature can only be used with "rigid" ligands (possessing few rotatable bonds). This feature is not yet integrated in Docking Server-but is going to be intergrated in our next release. If you need to carry out flexible docking, Virtua Drug (www.virtuadrug.com) is offering to carry out the docking calculation for you.


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