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J Comput Aided Mol Des. 2012 Jul;26(7):805-19. doi: 10.1007/s10822-012-9583-9. Epub 2012 Jun 4.

R-group template CoMFA combines benefits of "ad hoc" and topomer alignments using 3D-QSAR for lead optimization.

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1
Tripos DE, 1699 South Hanley Road, St. Louis, MO 63144, USA. Richard.Cramer@certara.com

Abstract

Template CoMFA methodologies extend topomer CoMFA by allowing user-designated templates, for example the experimental receptor-bound conformation of a prototypical ligand, to help determine the alignment of training and test set structures for 3D-QSAR. The algorithms that generate its new structural modality, template-constrained topomers, are described. Template CoMFA's resolution of certain topomer CoMFA concerns, by providing user control of topological consistency and structural acceptability, is demonstrated for sixteen 3D-QSAR training sets, in particular the Selwood dataset.

PMID:
22661224
DOI:
10.1007/s10822-012-9583-9
[Indexed for MEDLINE]
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