Computational Drug Discovery and Design

apt-cache search openbabel

Once the package is downloaded into the OS repository, it

can be installed by typing:

sudo apt-get install openbabel

Similarly, the same conveniences are available for Mac and

non-Debian-based Linux through MacPorts and yum tools,

respectively.

3. As a validation step for the methodology presented herein, it is
   suggested to always try to reproduce crystallographic confor-
   mations whenever they are available. In the absence of a crys-
   tallographic binding conformation, one molecule from the
   compound collection selected for the SBVS can be chosen for
   a preliminary molecular docking run. This approach is useful
   for generating the receptor input and providing an initial view
   of the structural peculiarities of the system under investigation.

Acknowledgments

We gratefully acknowledge financial support from the State of Sao

Paulo Research Foundation (FAPESP, Fundac ̧a ̃o de Amparo a`

Pesquisa do Estado de Sa ̃o Paulo), grants 2015/13667-9, 2013/

25658-9, and 2013/07600-3.

References

1. Jin L, Wang W, Fang G (2014) Targeting
   protein-protein interaction by small molecules.
   Annu Rev Pharmacol Toxicol 54:435–456


2. Blaney J (2012) A very short history of
   structure-based design: how did we get here
   and where do we need to go? J Comput
   Aided Mol Des 26:13–14


3. Kinch MS, Hoyer DA (2015) History of drug
   development in four acts. Drug Discov Today
   20:1163–1168


4. Kalyaanamoorthy S, Chen YP (2011)
   Structure-based drug design to augment hit
   discovery. Drug Discov Today 16:831–839


5. Honarparvar B, Govender T, Maguire GE et al
   (2014) Integrated approach to structure-based
   enzymatic drug design: molecular modeling,
   spectroscopy, and experimental bioactivity.
   Chem Rev 114:493–537


6. Eder J, Sedrani R, Wiesmann C (2014) The
   discovery of first-in-class drugs: origins and
   evolution. Nat Rev Drug Discov 13:577–587
   7. Shoichet BK, Kobilka BK (2012) Structure-
   based drug screening for G-protein-coupled
   receptors. Trends Pharmacol Sci 33:268–272
   8. Meng XY, Zhang HX, Mezei M, Cui M (2011)
   Molecular docking: a powerful approach for
   structure-based drug discovery. Curr Comput
   Aided Drug Des 7:146–157
   9. Kitchen DB, Decornez H, Furr JR et al (2004)
   Docking and scoring in virtual screening for
   drug discovery: methods and applications.
   Nat Rev Drug Discov 3:935–949


7. Ferreira LG, dos Santos RN, Oliva G et al
   (2015) Molecular docking and structure-
   based drug design strategies. Molecules
   20:13384–13421


8. Yuriev E, Agostino M, Ramsland PA (2011)
   Challenges and advances in computational
   docking: 2009 in review. J Mol Recognit
   24:149–164


9. McGann M (2012) FRED and HYBRID dock-
   ing performance on standardized datasets. J
   Comput Aided Mol Des 26:897–906

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