Journal of Computer-Aided Molecular Design

, Volume 29, Issue 10, pp 989–1006 | Cite as

Ultrafast protein structure-based virtual screening with Panther

  • Sanna P. Niinivehmas
  • Kari Salokas
  • Sakari Lätti
  • Hannu Raunio
  • Olli T. PentikäinenEmail author


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 ( free of charge after registration.


Molecular docking Panther Similarity search Virtual screening 



Androgen receptor


Area under curve


Directory of Useful Decoys


Directory of Useful Decoys: Enhanced


Enrichment factor


Estrogen receptor alpha


Glucocorticoid receptor


Merck molecular force field


Molecular Mechanics Generalized Born Area


Mineralocorticoid receptor


Negative image-based


Protein Data Bank


Peroxisome proliferator activated receptor gamma


Progesterone receptor


Root mean square deviation


Receiver operating characteristics


Retinoid X receptor alpha


Cyclo-oxygenase 2


Phosphodiesterase type 5



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).

Supplementary material

10822_2015_9870_MOESM1_ESM.pdf (639 kb)
Supplementary material 1 (PDF 638 kb)


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Copyright information

© Springer International Publishing Switzerland 2015

Authors and Affiliations

  • Sanna P. Niinivehmas
    • 1
  • Kari Salokas
    • 1
    • 2
  • Sakari Lätti
    • 1
    • 2
  • Hannu Raunio
    • 2
  • Olli T. Pentikäinen
    • 1
    Email author
  1. 1.Department of Biological and Environmental Science & Nanoscience CenterUniversity of JyvaskylaUniversity of JyvaskylaFinland
  2. 2.Faculty of Health Sciences, School of PharmacyUniversity of Eastern FinlandKuopioFinland

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