DOCK 3.5.54 is a substantially modified version of DOCK 3.5 used by the Shoichet Lab and available under the normal UCSF DOCK licensing terms (i.e. free to academics). All docking papers that have come out of this lab have used this program.
List of publications using DOCK 3.5.54
Many are directly cited on the Shoichet Lab Publications Page and referenced cited therein. It would be great if someone would format them nicely here.
List of publications of the methods in DOCK 3.5.54
- Kuntz, Shoichet 1993, here
- Shoichet & Lorber papers