The new features of DOCK 6 include: genetic algorithms and de novo design for fragment based ligand searching; additional scoring options during minimization; DOCK 3.5 scoring-including Delphi electrostatics, ligand conformational entropy corrections, ligand desolvation, receptor desolvation; Hawkins-Cramer-Truhlar GB/SA solvation scoring with ...

Nov 14, 2023 · DOCK 6 is an extension of the DOCK 5 code base. It includes the implementation of Hawkins-Cramer-Truhlar GB/SA solvation scoring with salt screening and PB/SA solvation scoring through OpenEye's Zap Library. Additional flexibility has been added to scoring options during minimization.

Tutorials for DOCK 6.11 . Rizzo et alia Tutorials . NOTE: These tutorials showcase the latest features and best practices from the currently most active DOCK developers. Lab Tutorials. Class Tutorials . Traditional Grid Score Tutorials

Nov 14, 2023 · The latest input from our user community dated January 2014 reports that DOCK version 6.6 was built on SGI machines running IRIX 6.5.23 and MIPSpro compiler version 7.4 from 2003. The sgi configuration files for DOCK versions …

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DOCK 6 is distributed for Unix versions compatible with the MPICH library, Linux, Windows, and MacIntosh OSX systems. DOCK 5 is distributed for Unix versions compatible with the MPICH library , Linux, Windows, and MacIntosh OSX systems.

With the release of DOCK 6, we continue to improve the algorithm's ability to predict binding poses by adding new features like force-field scoring enhanced by solvation and receptor flexibility. For more information about the current release of DOCK, click here .

Oct 7, 2023 · This tutorial describes the three steps required to define receptor active sites for DOCK calculations. We study the complex L-Arabinose-Binding Protein bound to L-Arabinose (PDB ID 1ABE) as an example system. However, these techniques should be transferable to any protein-ligand system.

DOCK 6.12 This is a release of DOCK6 with a new sampling method for hierarchical traversal through precomputed ligand conformations, as is done in DOCK 3.7. We have also updated the Chemgrid (DOCK3.5) scoring function to agree with DOCK3.7.

DOCK 6.10 This is a release of the version described in references [1] and [2] with the new genetic algorithm DOCK_GA: molecular evolution for ligand design.