A1 Refereed original research article in a scientific journal
Ultrafast protein structure-based virtual screening with Panther
Authors: Niinivehmas SP, Salokas K, Latti S, Raunio H, Pentikainen OT
Publisher: SPRINGER
Publication year: 2015
Journal: Journal of Computer-Aided Molecular Design
Journal name in source: JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
Journal acronym: J COMPUT AID MOL DES
Volume: 29
Issue: 10
First page : 989
Last page: 1006
Number of pages: 18
ISSN: 0920-654X
DOI: https://doi.org/10.1007/s10822-015-9870-3
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.
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.
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