How well do the substrates KISS the enzyme? Molecular docking program selection for feruloyl esterases

Publication: Research - peer-reviewJournal article – Annual report year: 2012

Standard

How well do the substrates KISS the enzyme? Molecular docking program selection for feruloyl esterases. / Udatha, D. B. R. K. Gupta; Sugaya, Nobuyoshi; Olsson, Lisbeth; Panagiotou, Gianni.

In: Scientific Reports, Vol. 2, 2012.

Publication: Research - peer-reviewJournal article – Annual report year: 2012

Harvard

APA

CBE

MLA

Vancouver

Author

Udatha, D. B. R. K. Gupta; Sugaya, Nobuyoshi; Olsson, Lisbeth; Panagiotou, Gianni / How well do the substrates KISS the enzyme? Molecular docking program selection for feruloyl esterases.

In: Scientific Reports, Vol. 2, 2012.

Publication: Research - peer-reviewJournal article – Annual report year: 2012

Bibtex

@article{95fc5cd9f90e4654a171a68acca429a5,
title = "How well do the substrates KISS the enzyme? Molecular docking program selection for feruloyl esterases",
keywords = "MULTIDISCIPLINARY, PROTEIN-STRUCTURE PREDICTION, VIRTUAL SCREENING ACCURACY, SCORING FUNCTIONS, I-TASSER, POSE PREDICTION, DRUG DISCOVERY, TOOLS, ALGORITHMS, ENRICHMENT, RECEPTORS",
publisher = "Nature Publishing Group",
author = "Udatha, {D. B. R. K. Gupta} and Nobuyoshi Sugaya and Lisbeth Olsson and Gianni Panagiotou",
year = "2012",
doi = "10.1038/srep00323",
volume = "2",
journal = "Scientific Reports",
issn = "2045-2322",

}

RIS

TY - JOUR

T1 - How well do the substrates KISS the enzyme? Molecular docking program selection for feruloyl esterases

A1 - Udatha,D. B. R. K. Gupta

A1 - Sugaya,Nobuyoshi

A1 - Olsson,Lisbeth

A1 - Panagiotou,Gianni

AU - Udatha,D. B. R. K. Gupta

AU - Sugaya,Nobuyoshi

AU - Olsson,Lisbeth

AU - Panagiotou,Gianni

PB - Nature Publishing Group

PY - 2012

Y1 - 2012

N2 - 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.

AB - 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.

KW - MULTIDISCIPLINARY

KW - PROTEIN-STRUCTURE PREDICTION

KW - VIRTUAL SCREENING ACCURACY

KW - SCORING FUNCTIONS

KW - I-TASSER

KW - POSE PREDICTION

KW - DRUG DISCOVERY

KW - TOOLS

KW - ALGORITHMS

KW - ENRICHMENT

KW - RECEPTORS

U2 - 10.1038/srep00323

DO - 10.1038/srep00323

JO - Scientific Reports

JF - Scientific Reports

SN - 2045-2322

VL - 2

ER -