I am working on a 3d molecular matching system using neural relaxation
(see my papers in ICANN '99, KES 2000, etc.). I am looking for some more
reference systems to compare my system against, but I am having problems
finding existing implementations of 3d molecular matching systems for
small molecules that are shareware of freeware. Can anyone point me to
any good sources? I have done various web searches, but tracking anything
down is rather difficult on the web these days.
I have a few implementations by a colleague of some other algorithms (EM,
Hodgkin scores, etc), but they are a little old now. Basically I am
looking for source code so I can control compilation to ensure I am using
the same levels of optimisation, etc, as my system to ensure a fair
comparasion. The problem I am aiming to solve is that of matching small
molecules against elements of a database of several tens of thousands of
Any hints/help would be greatly appreciated.
Advanced Compuer Architecture Group,
Department of Computer Science,
University of York.