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Comparative Data On Docking Algorithms: Keeping the Update in the Field Knowledge

Hioual K.S, Chikhi A, Bensegueni A, Merzoug A, Boucherit H Published in Algorithms

International Journal of Applied Information Systems
Year of Publication 2012
© 2010 by IJAIS Journal
10.5120/ijais12-450376
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  1. Merzoug A, Hioual K.s, Chikhi A, Bensegueni A and Boucherit H. Article: Comparative Data On Docking Algorithms: Keeping the Update in the Field Knowledge. International Journal of Applied Information Systems 2(7):27-31, May 2012. BibTeX

    @article{key:article,
    	author = "Merzoug A and Hioual K.s and Chikhi A and Bensegueni A and Boucherit H",
    	title = "Article: Comparative Data On Docking Algorithms: Keeping the Update in the Field Knowledge",
    	journal = "International Journal of Applied Information Systems",
    	year = 2012,
    	volume = 2,
    	number = 7,
    	pages = "27-31",
    	month = "May",
    	note = "Published by Foundation of Computer Science, New York, USA"
    }
    

Abstract

Two docking programs FlexX and GOLD that can be used for either single-ligand docking or database screening have been compared for their propensity to recover the X-ray pose of 153 pharmaceutically relevant protein-ligand complexes and for their capacity to discriminate known inhibitors of an enzyme from randomly chosen "druglike" molecules. Unfortunately, both properties are not found to be correlated since GOLD showing the best docking accuracy is the less successful in ranking known inhibitors in docking experiment. A speed comparison demonstrated that FlexX was thefastest. On the other hand, the best known docking algorithms often fail to position the ligand in anorientation close to the experimental binding mode this is what we call false positives, GOLD was shown to be the worst in ranking the top ten solutions. Moreover, the current study pinpoints one physicochemical descriptor of the ligand which is flexibility that generally lead to docking/scoring inaccuracies.

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Keywords

Docking Programs,flexx; Gold Database Screening, Compared, Druglike, Docking Accuracy, Speed, Docking/scoring