How well do the substrates KISS the enzyme? Molecular docking program selection for feruloyl esterases
Journal article, 2012

Molecular docking is the most commonly used technique in the modern drug discovery process where computational approaches involving docking algorithms are used to dock small molecules into macromolecular target structures. Over the recent years several evaluation studies have been reported by independent scientists comparing the performance of the docking programs by using default ‘black box’ protocols supplied by the software companies. Such studies have to be considered carefully as the docking programs can be tweaked towards optimum performance by selecting the parameters suitable for the target of interest. In this study we address the problem of selecting an appropriate docking and scoring function combination (88 docking algorithm-scoring functions) for substrate specificity predictions for feruloyl esterases, an industrially relevant enzyme family. We also propose the ‘Key Interaction Score System’ (KISS), a more biochemically meaningful measure for evaluation of docking programs based on pose prediction accuracy.


Gupta Udatha

Chalmers, Chemical and Biological Engineering, Industrial biotechnology

Nobuyoshi Sugaya

PharmaDesign, Inc.

Lisbeth Olsson

Wallenberg Wood Science Center (WWSC)

Chalmers, Chemical and Biological Engineering, Industrial biotechnology

Gianni Panagiotou

Technical University of Denmark (DTU)

Scientific Reports

2045-2322 (ISSN)

Vol. 2 Article number: 323-

Areas of Advance

Life Science Engineering (2010-2018)

Subject Categories

Bioinformatics and Systems Biology

Other Industrial Biotechnology



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