http://www.virtuadrug.com Just another WordPress site Tue, 03 Aug 2010 14:04:05 +0000 en hourly 1 http://www.virtuadrug.com/2esposztle/ http://www.virtuadrug.com/2esposztle/#comments Thu, 22 Jul 2010 12:28:48 +0000 hazaie http://www.virtuadrug.com/?p=98
read more..]]> Our featured product, DockingServer (http://www.dockingserver.com) offers a web-based, easy to use interface that handles all aspects of molecular docking calculations from ligand and protein set-up to evaluation and representation of the results. DockingServer integrates a number of computational chemistry software specifically aimed at correctly calculating parameters needed at different steps of the docking procedure, i.e. accurate ligand geometry optimization, energy minimization, charge calculation, docking calculation and protein-ligand complex representation. Thus, the use of DockingServer allows the user to carry out highly efficient and robust docking calculations by integrating a number of popular software used in in silico chemistry into one comprehensive web service.

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read more..]]> In the following paper, Virtua Drug has provided molecular modeling studies:
Functional adaptation of the switch-2 nucleotide sensor enables rapid processive translocation by myosin-5.
Nagy NT, Sakamoto T, Takács B, Gyimesi M, Hazai E, Bikádi Z, Sellers JR, Kovács M.
FASEB J. 2010 Jul 14.
Active site loops that are conserved across superfamilies of myosins, kinesins, and G proteins play key roles in allosteric coupling of NTP hydrolysis to interaction with track filaments or effector proteins. In this study, we investigated how the class-specific natural variation in the switch-2 active site loop contributes to the motor function of the intracellular transporter myosin-5. We used single-molecule, rapid kinetic and spectroscopic experiments and semiempirical quantum chemical simulations to show that the class-specific switch-2 structure including a tyrosine (Y439) in myosin-5 enables rapid processive translocation along actin filaments by facilitating Mg(2+)-dependent ADP release. Using wild-type control and Y439 point mutant myosin-5 proteins, we demonstrate that the translocation speed precisely correlates with the kinetics of nucleotide exchange. Switch-2 variants can thus be used to fine-tune translocation speed while maintaining high processivity. The class-specific variation of switch-2 in various NTPase superfamilies indicates its general role in the kinetic tuning of Mg(2+)-dependent nucleotide exchange

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