Drug efficiency indices for improvement of molecular docking scoring functions
Copyright 2009 Wiley Periodicals, Inc.
| Veröffentlicht in: | Journal of computational chemistry. - 1984. - 31(2010), 1 vom: 15. Jan., Seite 174-84 |
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| Format: | Online-Aufsatz |
| Sprache: | English |
| Veröffentlicht: |
2010
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| Zugriff auf das übergeordnete Werk: | Journal of computational chemistry |
| Schlagworte: | Comparative Study Journal Article Research Support, Non-U.S. Gov't Ligands Proteins |
| Zusammenfassung: | Copyright 2009 Wiley Periodicals, Inc. A dataset of protein-drug complexes with experimental binding energy and crystal structure were analyzed and the performance of different docking engines and scoring functions (as well as components of these) for predicting the free energy of binding and several ligand efficiency indices were compared. The aim was not to evaluate the best docking method, but to determine the effect of different efficiency indices on the experimental and predicted free energy. Some ligand efficiency indices, such as DeltaG/W (Wiener index), DeltaG/NoC (number of carbons), and DeltaG/P (partition coefficient), improve the correlation between experimental and calculated values. This effect was shown to be valid across the different scoring functions and docking programs. It also removes the common bias of scoring functions in favor of larger ligands. For all scoring functions, the efficiency indices effectively normalize the free energy derived indices, to give values closer to experiment. Compound collection filtering can be done prior or after docking, using pharmacokinetic as well as pharmacodynamic profiles. Achieving these better correlations with experiment can improve the ability of docking scoring functions to predict active molecules in virtual screening |
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| Beschreibung: | Date Completed 12.02.2010 Date Revised 11.03.2022 published: Print Citation Status MEDLINE |
| ISSN: | 1096-987X |
| DOI: | 10.1002/jcc.21306 |