How well do the substrates KISS the enzyme? Molecular docking program selection for feruloyl esterases
Artikel i vetenskaplig tidskrift, 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.

Författare

Gupta Udatha

Chalmers, Kemi- och bioteknik, Industriell Bioteknik

Nobuyoshi Sugaya

PharmaDesign, Inc.

Lisbeth Olsson

Chalmers, Kemi- och bioteknik, Industriell Bioteknik

Wallenberg Wood Science Center (WWSC)

Gianni Panagiotou

Danmarks Tekniske Universitet (DTU)

Scientific Reports

2045-2322 (ISSN)

Vol. 2 Article number: 323-

Styrkeområden

Livsvetenskaper och teknik

Ämneskategorier

Bioinformatik och systembiologi

Annan industriell bioteknik

DOI

10.1038/srep00323