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De Novo generation of molecular structures using optimization to select graphs on a given lattice

Authors
Publisher
American Chemical Society
Publication Date
Keywords
  • A Recurrent Problem In Organic Chemistry Is The Generation Of New Molecular Structures That Conform
  • An Example Of This Is The Pharmacophore Model
  • Used In Medicinal Chemistry To Guide De Novo Design Or Selection Of Suitable Structures From Compoun
  • We Propose Here A Method That Efficiently Links Up A Selected Number Of Required Atom Positions Whil
  • The Linkage Process Takes Place On A Lattice Whose Unit Step Length And Overall Geometry Is Designed
  • We Use An Optimization Method To Select From The Many Different Graphs Possible
  • The Approach Is Demonstrated In An Example Where Crystal Structures Of The Same (In This Case Rigid)
Disciplines
  • Biology
  • Chemistry
  • Design
  • Mathematics
  • Pharmacology

Abstract

De Novo generation of molecular structures using optimization to select graphs on a given lattice - DTU Orbit (18/06/14) De Novo generation of molecular structures using optimization to select graphs on a given lattice - DTU Orbit (18/06/14) De Novo generation of molecular structures using optimization to select graphs on a given lattice A recurrent problem in organic chemistry is the generation of new molecular structures that conform to some predetermined set of structural constraints that are imposed in an endeavor to build certain required properties into the newly generated structure. An example of this is the pharmacophore model, used in medicinal chemistry to guide de novo design or selection of suitable structures from compound databases. We propose here a method that efficiently links up a selected number of required atom positions while at the same time directing the emergent molecular skeleton to avoid forbidden positions. The linkage process takes place on a lattice whose unit step length and overall geometry is designed to match typical architectures of organic molecules. We use an optimization method to select from the many different graphs possible. The approach is demonstrated in an example where crystal structures of the same (in this case rigid) ligand complexed with different proteins are available. General information State: Published Organisations: Department of Mechanical Engineering, Department of Mathematics Authors: Bywater, R. (Ekstern), Poulsen, T. A. (Intern), Røgen, P. (Intern), Hjorth, P. G. (Intern) Pages: 856-861 Publication date: 2004 Main Research Area: Technical/natural sciences Publication information Journal: Journal of Chemical Information and Computer Sciences Volume: 44 Journal number: 3 ISSN (Print): 0095-2338 Original language: English DOIs: 10.1021/ci0342369 Source: orbit Source-ID: 135858 Publication: Research - peer-review › Journal article – Annual report year: 2004

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