Open3DQSAR is a freely available open-source program aimed at chemometric analysis of molecular interaction fields. MIFs can be imported from different sources (GRID, CoMFA/CoMSIA, quantum-mechanical electrostatic potential or electron density grids) or generated by Open3DQSAR itself. Much focus has been put on automation through the implementation of a scriptable interface, as well as on high computational performance achieved by algorithm parallelization. Flexibility and interoperability with existing molecular modeling software make Open3DQSAR a powerful tool in pharmacophore assessment and ligand-based drug design.
[Show abstract][Hide abstract] ABSTRACT: Drug discovery is currently driven by innovation and knowledge employing a combination of experimental and computational methods. Quantitative structure-activity relationships (QSAR) play a critical role in lead discovery and optimization, thus resulting in new drug candidates. 3D-QSAR methods use the information of the tridimensional molecular structure and can be generated to explain the relationships between the intermolecular interactions related to the 3D conformations of a set of structurally related molecules and their experimental activity, therefore, providing a rational basis for the development of new promising compounds. This review is intended to provide the reader with a perspective of the utility of 3D-QSAR approaches in drug design, highlighting the advances, challenges and future directions. The essential steps involved to generate reliable and predictive CoMFA models are discussed. Moreover, we present an example of application of a CoMFA study to derive 3D-QSAR models for a series of oxadiazoles inhibitors of Schistosoma mansoni Thioredoxin Glutathione Reductase (SmTGR).
Current Computer - Aided Drug Design 04/2014; 10(2). DOI:10.2174/1573409910666140410111043 · 1.27 Impact Factor
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