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AutoDock 4 Beta Release

by gillet last modified 2006-09-27 16:22

Release Note for AutoDock 4

AutoDock 4 is now available on a limited basis for beta testing. A selected number of users will be given a license for AutoDock4 beta.

 

In order to be considered for a beta license, please send e-mail to Prof. Arthur Olson (olson@scripps.edu), stating your prior experience with AutoDock and your willingness to provide user feedback during the beta test period.  If approved, you will then be sent the license to complete and return.  We will consider licenses for commercial companies for evaluation purposes only.
Once the beta test period is over, AutoDock 4.0 will become generally available.

What's new?

AutoDock 4.0 beta not only is it faster than earlier versions, it allows sidechains in the macromolecule to be flexible.  As before, rigid docking is blindingly fast, and high-quality flexible docking can be done in around a minute. Up to 40,000 rigid dockings can be done in a day on one cpu.

AutoDock 4.0 now has a free-energy scoring function that is based on a linear regression analysis, the AMBER force field, and an even larger set of diverse protein-ligand complexes with known inhibiton constants than we used in AutoDock 3.0. The best model was cross-validated with a separate set of HIV-1 protease complexes, and confirmed that the standard error is around 2.5 kcal/mol. This is enough to discriminate between leads with milli-, micro- and nano-molar inhibition constants.

AutoDock 4.0's search methods now include the optimization library, ACRO, from Bill Hart at Sandia National Labs.  We have added some new features to our existing evolutionary methods.  We still provide the Monte Carlo simulated annealing (SA) method of 2.4 and earlier.  The Lamarckian Genetic Algorithm (LGA) is a big improvement on the Genetic Algorithm, and both genetic methods are much more efficient and robust than SA.


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