Using protein homology models for structure-based studies: approaches to model refinement

Kairys, V.; Gilson, M. K.; Fernandes, Miguel Xavier

http://hdl.handle.net/10400.13/5003

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Authors

Kairys, V.

Gilson, M. K.

Fernandes, Miguel Xavier

Abstract(s)

Homology modeling is a computational methodology to assign a 3-D structure to a target protein when experimental data are not available. The methodology uses another protein with a known structure that shares some sequence identity with the target as a template. The crudest approach is to thread the target protein backbone atoms over the backbone atoms of the template protein, but necessary refinement methods are needed to produce realistic models. In this mini-review anchored within the scope of drug design, we show the validity of using homology models of proteins in the discovery of binders for potential therapeutic targets. We also report several different approaches to homology model refinement, going from very simple to the most elaborate. Results show that refinement approaches are system dependent and that more elaborate methodologies do not always correlate with better performances from built homology models.

Keywords

Homology modeling Docking Drug design Molecular dynamics . Faculdade de Ciências Exatas e da Engenharia

URI

http://hdl.handle.net/10400.13/5003

Citation

Kairys, V., Gilson, M. K., & Fernandes, M. X. (2006). Using protein homology models for structure-based studies: approaches to model refinement. TheScientificWorldJOURNAL, 6, 1542-1554.