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Ultrafast Algorithm for Designing Focused Combinational Arrays Dimitris K. Agrafiotis* and Victor S. Lobanov
 

Summary: Ultrafast Algorithm for Designing Focused Combinational Arrays
Dimitris K. Agrafiotis* and Victor S. Lobanov
3-Dimensional Pharmaceuticals, Inc., 665 Stockton Drive, Exton, Pennsylvania 19341
Received April 19, 2000
A novel greedy algorithm for the design of focused combinatorial arrays is presented. The method is applicable
when the objective function is decomposable to individual molecular contributions and makes use of a
heuristic that allows the independent evaluation and ranking of candidate reagents in each variation site in
the combinatorial library. The algorithm is extremely fast and convergent and produces solutions that are
comparable to and often better than those derived from the substantially more elaborate and computationally
intensive stochastic sampling techniques. Typical examples of design objectives that are amendable to this
approach include maximum similarity to a known lead (or set of leads), maximum predicted activity according
to some structure-activity or receptor binding model, containment within certain molecular property bounds,
and many others.
I. INTRODUCTION
Historically, drug discovery has been based on a serial
and systematic modification of chemical structure guided by
the "similar property principle",1 i.e., the assumption that
structurally similar compounds tend to exhibit similar phys-
icochemical and biological properties. New therapeutic
agents are typically generated by identifying a lead com-

  

Source: Agrafiotis, Dimitris K. - Molecular Design and Informatics Group, Johnson & Johnson Pharmaceutical Research and Development

 

Collections: Chemistry; Computer Technologies and Information Sciences