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J Comput Aided Mol Des. 2015 Oct;29(10):989-1006. doi: 10.1007/s10822-015-9870-3. Epub 2015 Sep 25.

Ultrafast protein structure-based virtual screening with Panther.

Author information

1
Department of Biological and Environmental Science & Nanoscience Center, University of Jyvaskyla, P.O. Box 35, 40014, University of Jyvaskyla, Finland.
2
Faculty of Health Sciences, School of Pharmacy, University of Eastern Finland, P.O. Box 1627, 70211, Kuopio, Finland.
3
Department of Biological and Environmental Science & Nanoscience Center, University of Jyvaskyla, P.O. Box 35, 40014, University of Jyvaskyla, Finland. olli.t.pentikainen@jyu.fi.

Abstract

Molecular docking is by far the most common method used in protein structure-based virtual screening. This paper presents Panther, a novel ultrafast multipurpose docking tool. In Panther, a simple shape-electrostatic model of the ligand-binding area of the protein is created by utilizing the protein crystal structure. The features of the possible ligands are then compared to the model by using a similarity search algorithm. On average, one ligand can be processed in a few minutes by using classical docking methods, whereas using Panther processing takes <1 s. The presented Panther protocol can be used in several applications, such as speeding up the early phases of drug discovery projects, reducing the number of failures in the clinical phase of the drug development process, and estimating the environmental toxicity of chemicals. Panther-code is available in our web pages (http://www.jyu.fi/panther) free of charge after registration.

KEYWORDS:

Molecular docking; Panther; Similarity search; Virtual screening

PMID:
26407559
DOI:
10.1007/s10822-015-9870-3
[Indexed for MEDLINE]

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