How to optimize shape-based virtual screening: choosing the right query and including chemical information
| Autor: | Gudrun M. Spitzer, Gerhard Wolber, Daniela Schuster, Klaus R. Liedl, Simona Distinto, Johannes Kirchmair, Patrick Markt |
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| Rok vydání: | 2009 |
| Předmět: |
Structure (mathematical logic)
Virtual screening Similarity (geometry) business.industry Computer science Computers General Chemical Engineering Chemistry Pharmaceutical General Chemistry Directory Library and Information Sciences computer.software_genre Antithrombins Computer Science Applications Set (abstract data type) Software Benchmark (computing) Data mining business computer Selection (genetic algorithm) |
| Zdroj: | Journal of chemical information and modeling. 49(3) |
| ISSN: | 1549-9596 |
| Popis: | Shape-based molecular similarity approaches have been established as important and popular virtual screening techniques. Recent applications have shown successful screening campaigns using different parameters and query selection. It is common sense that pure volume overlap scoring (or “shape-based screening”) under-represents chemical or pharmacophoric information of a molecule. Using the “Directory of Useful Decoys” (DUD) as a benchmark set, we systematically evaluate how (i) the choice of query conformations, (ii) the selection of the active compound to be used as a query structure, and (iii) the inclusion of chemical information (i.e., the pharmacophoric properties of the query molecule) affect screening performance. Varying these parameters bears remarkable potential for improvements and delivers the best screening performance reported using these tools so far. From these insights, guidelines on how to reach optimum performance during virtual screening are developed. |
| Databáze: | OpenAIRE |
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