From DISI

UCSF DOCK is a computer program for molecular docking, the process of orienting and scoring small molecules in a macromolecular (usually protein) binding site. Started in the early 1980s by Tack Kuntz and his group, DOCK was the first of many such programs, and has been in widespread use for over 20 years.

The official website for all versions of DOCK, including the most recent one, is dock.compbio.ucsf.edu. There is a discussion group.

Several versions of DOCK

DOCK has been completely re-written twice. Each re-write has not entirely superceded the previous version, and thus several versions continue to be available. The official goal is to merge the best features of all DOCK versions into a single program. Whereas DOCK 5 is entirely superceded by DOCK 6, DOCK 4 has a few features still not available in DOCK 6. Since many papers have appeared based on DOCK 4, we will continue to make it available. DOCK 3.5.54, a version of DOCK 3.5, is used by the DOCK Blaster service, and is the version we use for our research. Many but not all of its capabilities have been incorporated into DOCK 6, and thus it is still available.

It is our official policy to merge all features into a single DOCK program, but goal has so far eluded us. For the longer version of the history of DOCK, please see History.

List of available versions

• DOCK 6 - 2006-present, the latest version is DOCK 6.1 (released December 2006). This is the "flagship" version. It is a long term goal to consolidate the features from all other versions into this one. DOCK 6.2 is reported nearly ready (Dec 07). Watch for it.

• DOCK 5 - 2000-2005, DOCK 5 was a complete re-write of DOCK in C++. Although DOCK 5 is still available, its use is *deprecated*.

• DOCK 4 - 1998-2002, DOCK 4 was a complete re-write of DOCK in C. Although DOCK 4 is still available, its use is *deprecated*.

• DOCK 3.5.54 - 1993 - present, DOCK 3.5.54 is the latest version of this FORTRAN-coded software. It is the engine behind DOCK Blaster.

• DOCK (1) DOCK 2, DOCK 2.5, DOCK 3 - circa 1980 - 1994. These versions of DOCK were entirely superseded by DOCK 3.5 (1994). Well, ok, you want to nitpick? There were reportedly some features in 2.5 that did not make it into 3. It is alledged that there is a fanatical DOCK 2.5 following somewhere. If you meet one of them ask them to send us a postcard.