DOCK 6

DOCK 6 is a general purpose molecular docking program developed by the Kuntz Laboratory at UCSF. DOCK 6 (released summer 2006) replaced DOCK 5 (2001-2006), which is no longer available. DOCK 5 was a complete re-write 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 mainly in C++. Using the object oriented model, 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 512 MB RAM. Some runs may require considerably more disk space and more memory.

• DOCK website
• Licensing
• 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 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