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Ultrafast protein structure-based virtual screening with Panther
Tekijät: Niinivehmas SP, Salokas K, Latti S, Raunio H, Pentikainen OT
Kustantaja: SPRINGER
Julkaisuvuosi: 2015
Journal: Journal of Computer-Aided Molecular Design
Tietokannassa oleva lehden nimi: JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
Lehden akronyymi: J COMPUT AID MOL DES
Vuosikerta: 29
Numero: 10
Aloitussivu: 989
Lopetussivu: 1006
Sivujen määrä: 18
ISSN: 0920-654X
DOI: https://doi.org/10.1007/s10822-015-9870-3
Tiivistelmä
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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