Practices in Molecular Docking and Structure-Based Virtual Screening

  • Ricardo N. dos Santos
  • Leonardo G. Ferreira
  • Adriano D. Andricopulo
Part of the Methods in Molecular Biology book series (MIMB, volume 1762)


Drug discovery has evolved significantly over the past two decades. Progress in key areas such as molecular and structural biology has contributed to the elucidation of the three-dimensional structure and function of a wide range of biological molecules of therapeutic interest. In this context, the integration of experimental techniques, such as X-ray crystallography, and computational methods, such as molecular docking, has promoted the emergence of several areas in drug discovery, such as structure-based drug design (SBDD). SBDD strategies have been broadly used to identify, predict and optimize the activity of small molecules toward a molecular target and have contributed to major scientific breakthroughs in pharmaceutical R&D. This chapter outlines molecular docking and structure-based virtual screening (SBVS) protocols used to predict the interaction of small molecules with the phosphatidylinositol-bisphosphate-kinase PI3Kδ, which is a molecular target for hematological diseases. A detailed description of the molecular docking and SBVS procedures and an evaluation of the results are provided.

Key words

Autodock vina Drug discovery Molecular modeling Structure-based drug design X-ray crystallography 



We gratefully acknowledge financial support from the State of Sao Paulo Research Foundation (FAPESP, Fundação de Amparo à Pesquisa do Estado de São Paulo), grants 2015/13667-9, 2013/25658-9, and 2013/07600-3.


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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Departamento de Físico-QuímicaUniversidade Estadual de Campinas (UNICAMP)CampinasBrazil
  2. 2.Laboratório de Química Medicinal e Computacional, Centro de Pesquisa e Inovação em Biodiversidade e Fármacos, Instituto de Física de São CarlosUniversidade de São Paulo (USP)São CarlosBrazil

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