ADL: Perspective on AutoDock Vina
trott at scripps.edu
Tue Nov 27 14:27:13 PST 2012
On Tue, Nov 27, 2012 at 4:36 AM, Marian and Eric Smidansky
<eandms1977 at comcast.net> wrote:
> 2. What motivated you to write Vina in light of the popularity and success of the "standard" AutoDock 4?
I wanted to make improvements to the search algorithm and make it
parallel. I thought I could do better in the software engineering
aspect of the design as well, so I decided to write the code from
scratch, rather than trying to retrofit the improvements on AutoDock
4. Today, AutoDock/AutoGrid source code weighs in at 41k lines, and
Vina at just 9k lines, despite Vina implementing a substantially more
sophisticated algorithm, with gradient and parallelism (The number of
lines of code is a flawed metric, of course, but it's objective)
> 1. What is the meaning or significance of the name "Vina"? Why was this name chosen and what does it mean in the context of docking?
I called the program "AutoBind" in its early development stages,
following the naming pattern of other projects in MGL (AutoDock,
AutoGrid, AutoLigand, AutoDock Tools), and I announced at a lab
meeting that I was hoping to make vast algorithmic improvements with
an independent implementation. The author of the original (20+ year
old) FORTRAN AutoDock code, David Goodsell, then asked me to change
the name to something that wasn't "Auto".
I then chose the name "Vina" because it's an English word and, at the
same time, a self-referential acronym for "VINA Is Not Auto[Dock]".
This is the name under which the program was initially released.
Later on, the head of the lab and the P.I. on the AutoDock grant,
Arthur Olson, asked me to change the name from "Vina" to "AutoDock
Oleg Trott, Ph.D. (Columbia University)
Staff Scientist in the Olson Lab
The Scripps Research Institute
More information about the autodock