Molecular Docking Server
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Protein Conformation
https://www.dockingserver.com/forum/viewtopic.php?f=6&t=5
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Author:  owenmcdougal [ Thu Jan 29, 2009 3:16 am ]
Post subject:  Protein Conformation

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.

Author:  hazaie [ Thu Jan 29, 2009 10:15 am ]
Post subject:  Re: Protein Conformation

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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