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BACKGROUND

Computational drug design and discovery has been a challenging task due to limitations in available computing resources. Public cloud computing facilities have dramatically changed this scenario, by bringing the most powerful computing systems within a click away, with unprecedented low cost options.

OBJECTIVES

This hands-on training will introduce researchers to the concepts, methods and tools for structure and ligand based computational drug designing and discovery using the open source tools and the cloud computing facilities.

Tools/Skills to be Taught (tentative):

Ligand preparation: OpenBabel
Target preparation: Chimera
Databases: ZINC, PubChem, ChemSpider, ChEMBL, DrugBank, Binding DB
Docking: AutoDockTools
Visualization: Chimera, PyMOL
Structure based virtual screening: AutoDock, Dock
Ligand drawing & visualization: Chemdraw, Chemsketch
Compound library: ChemT (or DRUGSTER or FSees)
Descriptors: Mold2
QSAR: Open3DQSAR (or TEST or Coral)
Pharmacophore exploration: Open3DQSAR (or DRUGON or pharmacophore)
Ligand alignment: LIGSIFT
Ligand based virtual screening: LIGSIFT (or MOLA or lisica)
ADMET, Toxicity estimation: Toxtree (or DataWarrior)

Discussion forums: Education: Training in Computational Drug Design and Discovery @ NIH

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