DOCK 6

DOCK 6 is a general purpose molecular docking program developed by the Kuntz Laboratory at UCSF. DOCK 6 (released summer 2006) is a significant upgrade of DOCK 5 (2001-2006), which in turn was a complete rewrite and redesign of DOCK 4 (1998-2002), which itself was a complete re-design and re-write of DOCK 3.5 (released 1993-1994).

DOCK 6 is coded predominantly in C++. It is functionally separated into independent components (classes, methods), allowing a high degree of modularity and programming flexibility. Accessory programs are written in a variety of languages including C and Fortran 77. Source code is available for all programs. The DOCK suite of programs requires on the order of 50 MB of disk space and 256 MB RAM. Some runs may require considerably more disk space.

• Official DOCK website
• Licensing (allow up to 7 days for reply)
• Manual as a single PDF. File:Dock61.pdf
• Tutorials
• Test sets
• DOCK:FAQ

New Features in DOCK 6

• additional scoring options during minimization;
• DOCK 3.5.54 scoring, including Delphi electrostatics
• ligand conformational entropy corrections
• ligand desolvation
• receptor desolvation
• Hawkins-Cramer-Truhlar GB/SA solvation scoring with optional salt screening
• PB/SA solvation scoring
• AMBER scoring, including
  • receptor flexibility
  • the full AMBER molecular mechanics scoring function with
    • implicit solvent
    • conjugate gradient minimization
    • and molecular dynamics simulation capabilities.

Manual

• DOCK:Introduction
• DOCK:Installation
• DOCK:Site preparation
• DOCK:Sampling
• DOCK:Scoring
• DOCK:Input
• DOCK:Output
• DOCK:Parameters
• DOCK:Parallelism
• DOCK:Accessories
• DOCK:File formats
• DOCK:References