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Interaction Fingerprints and Their Applications to Identify Hot Spots

  • Andrés F. Marmolejo
  • José L. Medina-Franco
  • Marc Giulianotti
  • Karina Martinez-MayorgaEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1335)

Abstract

Binding recognition is in the core of how nature controls processes in living cells, how enzyme–substrate binding leads to catalysis and how drugs modulate enzymes and receptors to convey a desirable physiological response. Thus, understanding binding recognition in a systematic manner is paramount, not only to understand biological processes but also to be able to design and discover new bioactive compounds. One such way to analyze binding interactions is through the development of binding interaction fingerprints. Here, we present the methodology to develop interaction fingerprints with three different software platforms along with two representative examples.

Key words

Protein–ligand interactions Interaction fingerprints Kinases Opioid receptors 

Notes

Acknowledgments

KMM acknowledge Institute of Chemistry and PAPIIT IA200513-2 for financial support. JLMF thanks the Department of Pharmacy, School of Chemistry at UNAM for support. This work was partially supported by the State of Florida, Executive Officer of the Governor’s Department of Economic Development.

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Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  • Andrés F. Marmolejo
    • 1
  • José L. Medina-Franco
    • 2
  • Marc Giulianotti
    • 3
  • Karina Martinez-Mayorga
    • 1
    Email author
  1. 1.Instituto de QuímicaUniversidad Nacional Autónoma de MéxicoMexico CityMexico
  2. 2.Facultad de Química, Departamento de FarmaciaUniversidad Nacional Autónoma de MéxicoMéxico D. F.Mexico
  3. 3.Torrey Pines Institute for Molecular StudiesPort St. LucieUSA

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