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.
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
http://science.nas.nasa.gov/Pubs/NASnews/96/08/invention.html
Gina "Nanogirl" Miller
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.
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E-mail:
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