From: Gina Miller (nanogirl@halcyon.com)
Date: Wed May 12 1999 - 17:15:55 MDT
UCSC's INVENTON Software Creates Molecules in 3D
by Elisabeth Wechsler
A software package under development at the University of California, Santa
Cruz (UCSC) uses artificial intelligence techniques and a knowledge of
chemistry to "invent" molecules in 3D space -- something that has been
lacking to date, according to Professor Todd Wipke, of UCSC's Molecular
Engineering Laboratory.
"Chemists have no good algorithms for manually enumerating the molecules
that can satisfy a set of constraints in 3D," he said, in his March 5th
presentation at the NAS Computational Molecular Nanotechnology Workshop.
Wipke believes that "computers, when properly programmed, [can] be more
creative than chemists in the task of inventing new chemical structures."
Called INVENTON, the program automatically constructs chemical frameworks
that position atoms in a desired 3D arrangement, giving researchers new
ideas for building blocks. Wipke summarized the paradigm as: "Chemist
describes objectives and constraints. Computer formulates strategy and
tactics, then invents structures and ranks them. Chemist reviews resulting
candidates." More specifically, INVENTON creates molecules by adding
molecular fragments to span the space from one point to another. The points
are given in the problem description provided by the chemist or are
generated as subgoals. The molecular fragments come from a basis set
established by the investigator. INVENTON also can build structures from
individual atoms. Finally, the program ranks the candidate structures by
scoring functions selected by the chemist, Wipke explained.
Productive Approach To Design
"A computer program can invent molecules that have never been conceived of
and do not exist in any database anywhere," he commented. In its six years
of existence, INVENTON has designed structures in the domains of
nanotechnology (self-assembling molecules in nanoscale systems) and
pharmaceutical drugs (such as mimics of known drugs for cancer and enzyme
inhibitors for AIDS).
"Designing a system like this is a complex task -- one that requires really
logical thinking. AI methods are already being used by INVENTON to
prioritize tasks, and heuristic search is used to reduce the number of
`relevant' constraints." In addition, bringing "engineering principles
across boundaries to assist chemical design" has been useful, Wipke noted.
Automated molecular design will benefit from greater CPU speed, more
knowledge and understanding, and larger organized collections of chemical
information readable by computer, he said, adding that "having more complex
problems will accelerate our abilities to problem solve."
Collaboration with NAS
Collaborative work between Wipke's group at UCSC and Al Globus (NAS
applications and tools group) has included modifications to the search
strategy and solving simple initial problems. Current work is focused on
developing fragment libraries designed for nanotechnology and then applying
them to problems requiring very stiff molecules. A more difficult future
problem is taking advantage of the high degree of symmetry common in
nanotechnology problems and spanning space with molecular fragments that can
be repeated an indefinite number of times.
http://science.nas.nasa.gov/Pubs/NASnews/96/08/invention.html
Gina "Nanogirl" Miller
Nanotechnology Industries
Web:
http://www.nanoindustries.com
E-mail:
nanogirl@halcyon.com
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