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Web Services for Molecular Docking Simulations

  • Nelson J. F. da Silveira
  • Felipe Siconha S. Pereira
  • Thiago C. Elias
  • Tiago Henrique
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 2053)

Abstract

Docking process is one of the most significant activities for the analysis of protein–protein or protein–ligand complexes. These tools have become of unique importance when allocated in web services, collaborating scientifically with several areas of knowledge in an interdisciplinary way. Among the several web services dedicated to carrying out molecular docking simulations, we selected the DockThor web service. To illustrate the application of DockThor to protein–ligand docking simulations, we analyzed the docking of a ligand against the structure of epidermal growth factor receptor, an essential molecular marker in cancer research.

Key words

Web docking Web services Docking affinity Score function Complex Protein–protein Protein–ligand 

Notes

Acknowledgments

This work was supported by LNCC/MCTIC, SINAPAD, INCT-Inofar, FAPERJ, CNPq, and CAPES.

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Nelson J. F. da Silveira
    • 1
  • Felipe Siconha S. Pereira
    • 2
  • Thiago C. Elias
    • 1
  • Tiago Henrique
    • 3
  1. 1.Laboratory of Molecular Modeling and Computer Simulation/MolMod-CS, Institut of Exact Science/ICExFederal University of Alfenas/UNIFAL-MGAlfenasBrazil
  2. 2.Laboratory of Computacional Modeling, National Laboratory of Scientific Computing (LNCC)PetrópolisBrazil
  3. 3.Departament of Molecular BiologyMedical School of São José do Rio Preto/FAMERPSão José do Rio PretoBrazil

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