PMID: 8594156Oct 1, 1995Paper

PRO_LIGAND: an approach to de novo molecular design. 6. Flexible fitting in the design of peptides

Journal of Computer-aided Molecular Design
C W MurrayD G Byrne

Abstract

This paper describes the further development of the functionality of our in-house de novo design program, PRO_LIGAND. In particular, attention is focused on the implementation and validation of the 'direct tweak' method for the construction of conformationally flexible molecules, such as peptides, from molecular fragments. This flexible fitting method is compared to the original method based on libraries of prestored conformations for each fragment. It is shown that the directed tweak method produces results of comparable quality, with significant time savings. By removing the need to generate a set of representative conformers for any new library fragment, the flexible fitting method increases the speed and simplicity with which new fragments can be included in a fragment library and also reduces the disk space required for library storage. A further improvement to the molecular construction process within PRO_LIGAND is the inclusion of a constrained minimisation procedure which relaxes fragments onto the design model and can be used to reject highly strained structures during the structure generation phase. This relaxation is shown to be very useful in simple test cases, but restricts diversity for more realistic examples. Th...Continue Reading

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Citations

Oct 1, 1996·Journal of Computer-aided Molecular Design·D E ClarkC W Murray
Jun 8, 2011·Journal of Computer-aided Molecular Design·Tsung-Ying TsaiCalvin Yu-Chian Chen
Sep 13, 2001·Journal of Molecular Graphics & Modelling·J PeiX He
Aug 2, 2005·Nature Reviews. Drug Discovery·Gisbert Schneider, Uli Fechner
Nov 1, 1996·Journal of Chemical Information and Computer Sciences·Z LuoL Lai
Aug 9, 2019·Journal of Chemical Information and Modeling·Hsuan-Hao HsuShiang-Tai Lin

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