Subject: Re: CCL:PLP - piecewise linear potential?

From: Richard Gillilan <[email-masked]>
Date: Fri, 08 Oct 1999 09:44:30 -0400

Joe M Leonard wrote:
> 
> Folks,
> 
> I am trying to parse my notes from ACS, New Orleans, and I wonder
> whether anybody has references to the PLP docking/scoring function
> which was mentioned by several speakers.  I think this is the
> "piecewise linear potential" method, but I'm not sure of this...
> 

The idea is simple. Just pre-evaluate the potential on a grid and
use trilinear interpolation. Several docking programs out there use
piecewise
linear approximations to the potential (or forces) on a regular grid:

    Autodock (Goodsell and Olson)
        Proteins: Structure, Function and Genetics 8:195-202 (1990)

    FlexX (Luty, Wasserman, Stouten and Hodge)
         J. Comp. Chem. Vol 16, No 4 454-464 (1995)

   (I'm pretty sure there are several others, but I can't find the refs
    at the moment. The method has also been used in material science 
    simulations)

Also, Oberlin, Trosset and Scheraga have used cubic B-splines on a
regular grid
with great success (Prodock). This method allows for larger grid
elements with
better accuracy, C2 continuity (smooth derivatives) and overall greater
smoothness
which seems to improve the search efficiency:

Oberlin, Scheraga  J. Comp. Chem. Vol 19 No 1 pp 71-85 (1998)
Trosset, Scheraga  J. Comp. Chem. Vol 20 No 4 pp 412-427 (1999)

I've implemented this technique in OrderFour, my own MMFF-based docking
and
simulation code. I'm also experimenting with adaptive and hierarchical
grids
for use in multi-body protein-protein docking. OrderFour will be
generally available
as open-source (I will read-enable the revision control system) as soon
as I can get 
a paper out and get final approval from CTC. We are still making major
revisions to
the API so it's still too early to invite external users to help work on
the code, but 
I'll make a general announcement when things are ready some time this
winter.

Richard

Richard Gillilan  ([email-masked])
Cornell Theory Center