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An alternative method for the evaluation of docking performance: RSR vs RMSD.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structural Molecular Biology.
2008 (English)In: Journal of chemical information and modeling, ISSN 1549-9596, Vol. 48, no 7, 1411-1422 p.Article in journal (Refereed) Published
Abstract [en]

A new assessment criterion for docking poses is proposed in which experimental electron density is taken into account when evaluating the ability of docking programs to reproduce experimentally observed binding modes. Three docking programs (Gold, Glide, and Fred) were used to generate poses for a set of 88 protein-ligand complexes for which the crystal structure is known. The new criterion is based on the real space R-factor (RSR), which measures how well a group of atoms-in our case the ligand-fits the experimental electron density by comparing that density to the expected density, calculated from the model (i.e., the predicted ligand pose). The RSR-based measure is compared to the traditional criterion, the root-mean-square distance (RMSD) between the docking pose and the binding configuration in the crystallographic model. The results highlight several shortcomings of the RMSD criterion that do not affect the RSR-based measure. Examples illustrate that the RSR-derived approach allows a more meaningful a posteriori assessment of docking methods and results. Practical implications for docking evaluations and for methodological development work in this field are discussed.

Place, publisher, year, edition, pages
2008. Vol. 48, no 7, 1411-1422 p.
Identifiers
URN: urn:nbn:se:uu:diva-105993DOI: 10.1021/ci800084xPubMedID: 18598022OAI: oai:DiVA.org:uu-105993DiVA: diva2:223144
Available from: 2009-06-11 Created: 2009-06-11 Last updated: 2009-07-02Bibliographically approved

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