Concept and Applications of Pseudoreceptors

This chapter does not cover these classical approaches but rather focuses on basic principles, evolution and scientific applications based on specialized pseudoreceptor modeling software packages. 

Pharmacophores and Pharmacophore Searches. Edited byT. Langer and R. D. Hoffmann Copyright 2006 WILEY-VCH Verlag GmbH Co. KGaA, Weinheim ISBN 3-527-31250-1 

In order to build up an atomistic pseudoreceptor model, the following basic steps have to be carried out  

If individually positioned residues are in close contact, the program evaluates the possibility of peptide-bond formation and thus links single residues to a peptide. Furthermore, ligand-independent extension (i.e. residues without direct contact to vectors) of the pseudoreceptor can be used in order to complete the peptidic receptor site (e.g. entirely closed shell around the ligand molecules). 

Internal ligand relaxation allows the removal of strain possibly imposed on the ligands by the receptor during correlation-coupled refinement but usually yields suboptimal models. Therefore, correlation-coupled receptor minimization followed by unconstrained ligand relaxation is repeated several times until a highly correlated pseudoreceptor model is obtained in the relaxed state (designated ligand equilibration). 

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