Open3DQSAR: A new open-source software aimed at high-throughput chemometric analysis of molecular interaction fields

Department of Drug Science, University of Torino, Via Pietro Giuria 9, 10125 Torino, Italy.
Journal of Molecular Modeling (Impact Factor: 1.74). 04/2010; 17(1):201-8. DOI: 10.1007/s00894-010-0684-x
Source: PubMed


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.
Open3DQSAR’s logo displaying PLS coefficient isocontours

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    • "The steric and electrostatic CoMFA potential fields were performed using Open3DQSAR ( Tosco and Balle , 2011 ) . MOE 2007 . "
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    ABSTRACT: The quinoline moiety is one of the widely studied scaffolds for generating derivatives with various pharmacophoric groups due to its potential antimalarial activities. In the present study, a series of 7-substituted-4-aminoquinoline derivatives were selected to understand their antimalarial properties computationally by molecular modeling techniques including 2D QSAR, comparative molecular field analysis (CoMFA), comparative molecular similarity indices analysis (CoMSIA) and molecular docking. The 2D-QSAR model built with four descriptors selected by genetic algorithm technique and CoMFA model showed satisfactory statistical results (Q(2) = 0.540, R(2)ncv = 0.881, F value = 157.09). A reliable CoMSIA model out of the fourteen different combinations has a Q(2) value of 0.638. The molecular docking studies of the compounds for 1CET as the protein target revealed that ten compounds showed maximum interactions with the binding site of the protein. The present study highlights the unique binding signatures of the ligands within the active site groove of the target and it explains the subtle differences in their EC50 values and their mechanism of inhibition. Copyright © 2015. Published by Elsevier B.V.
    Full-text · Article · Sep 2015 · European journal of pharmaceutical sciences: official journal of the European Federation for Pharmaceutical Sciences
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    • "Open3DQSAR is an open-source software in which MIFs are analyzed by chemometric approaches [53]. Firstly, the 3D coordinates of the compounds can be loaded and MIFs calculated in Open3DQSAR. "
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    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).
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