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Recent advances in de novo ligand design and optimisation

Krisztina Boda, A. Peter Johnson, Shane Weaver, Aniko T. Vigh, Vilmos A. Valko
School of Chemistry
University of Leeds
Leeds, LS2 9JT
United Kingdom
Presentation held at:
7th International Conference on Chemical Structures
June 2005, Noordwijkerhout, The Netherlands

Systems which purport to carry out the protein structure based de novo design of ligands have now been available for over a decade. The extent to which this goal is achieved varies widely, and there are still many problems waiting to be solved in this area. The presentation will review some of these problems and discuss some of the solutions which have been developed in our laboratory. Areas covered will include: a) conformational sampling in structure generation b) methods for optimisation of existing ligands by automatic structure modification taking into account availability of starting materials c) navigation of answer sets using structural complexity analysis.