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Sensitivity of an Empirical Affinity Scoring Function to Changes in Receptor-Ligand Complex Conformations
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structural Molecular Biology.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structural Molecular Biology.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structural Molecular Biology.
2001 (English)In: European Journal of Pharmaceutical Sciences, ISSN 0928-0987, E-ISSN 1879-0720, Vol. 14, no 1, p. 87-95Article in journal (Refereed) Published
Abstract [en]

A combination of empirical scoring and conformational sampling for ligand bindingaffinity prediction is examined. The behaviour of a scoring function with respect to thesensitivity to conformational changes is investigated using ensembles of structures generated by molecular dynamics simulation. The correlation between the calculated score and the coordinate deviation from the experimental structure is clear for the complex of arabinose with arabinose-binding protein, which is dominated by hydrogen bond interactions, while the score calculated for the hydrophobic complex between retinol and retinol binding protein is rather insensitive to ligand conformational changes. For typical ensembles of stuctures generated by molecular dynamics at 300 K. the variation of the calculated score is considerably smaller than that of the underlying molecular mechanics interaction energies.

Place, publisher, year, edition, pages
2001. Vol. 14, no 1, p. 87-95
National Category
Medical and Health Sciences Natural Sciences
Identifiers
URN: urn:nbn:se:uu:diva-45335DOI: 10.1016/S0928-0987(01)00162-2ISI: 000170180600012OAI: oai:DiVA.org:uu-45335DiVA, id: diva2:73242
Available from: 2006-03-15 Created: 2006-03-15 Last updated: 2017-12-05Bibliographically approved

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Ljungberg, KajsaÅqvist, J

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