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Ultrafast protein structure-based virtual screening with Panther

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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.

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Abbreviations

AR:

Androgen receptor

AUC:

Area under curve

DUD:

Directory of Useful Decoys

DUD-E:

Directory of Useful Decoys: Enhanced

EF:

Enrichment factor

ERα:

Estrogen receptor alpha

GR:

Glucocorticoid receptor

MMFF:

Merck molecular force field

MMGBSA:

Molecular Mechanics Generalized Born Area

MR:

Mineralocorticoid receptor

NIB:

Negative image-based

PDB:

Protein Data Bank

PPARγ:

Peroxisome proliferator activated receptor gamma

PR:

Progesterone receptor

RMSD:

Root mean square deviation

ROC:

Receiver operating characteristics

RXRα:

Retinoid X receptor alpha

COX2:

Cyclo-oxygenase 2

PDE5:

Phosphodiesterase type 5

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Acknowledgments

This work was financially supported by National Doctoral Programme in Nanoscience (SPN) and Academy of Finland (HR). CSC, The Finnish IT Center for Science is acknowledged for computational resources (OTP; Project Nos. jyy2516 and jyy2585).

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Authors and Affiliations

  1. Department of Biological and Environmental Science & Nanoscience Center, University of Jyvaskyla, P.O. Box 35, 40014, University of Jyvaskyla, Finland

    Sanna P. Niinivehmas, Kari Salokas, Sakari Lätti & Olli T. Pentikäinen

  2. Faculty of Health Sciences, School of Pharmacy, University of Eastern Finland, P.O. Box 1627, 70211, Kuopio, Finland

    Kari Salokas, Sakari Lätti & Hannu Raunio

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  1. Sanna P. Niinivehmas
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Correspondence to Olli T. Pentikäinen.

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Niinivehmas, S.P., Salokas, K., Lätti, S. et al. Ultrafast protein structure-based virtual screening with Panther. J Comput Aided Mol Des 29, 989–1006 (2015). https://doi.org/10.1007/s10822-015-9870-3

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