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3-D QSAutogrid/R: an alternative procedure to build 3-D QSAR models. Methodologies and applications.
Rome Center for Molecular Design, Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, P. le A. Moro 5, 00185, Rome, Italy.ORCID iD: 0000-0002-4831-3423
Rome Center for Molecular Design, Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, P. le A. Moro 5, 00185, Rome, Italy.
2012 (English)In: Journal of Chemical Information and Modeling, ISSN 1549-9596, E-ISSN 1549-960X, Vol. 52, no 6, 1674-85 p.Article in journal (Refereed) Published
Abstract [en]

Since it first appeared in 1988 3-D QSAR has proved its potential in the field of drug design and activity prediction. Although thousands of citations now exist in 3-D QSAR, its development was rather slow with the majority of new 3-D QSAR applications just extensions of CoMFA. An alternative way to build 3-D QSAR models, based on an evolution of software, has been named 3-D QSAutogrid/R and has been developed to use only software freely available to academics. 3-D QSAutogrid/R covers all the main features of CoMFA and GRID/GOLPE with implementation by multiprobe/multiregion variable selection (MPGRS) that improves the simplification of interpretation of the 3-D QSAR map. The methodology is based on the integration of the molecular interaction fields as calculated by AutoGrid and the R statistical environment that can be easily coupled with many free graphical molecular interfaces such as UCSF-Chimera, AutoDock Tools, JMol, and others. The description of each R package is reported in detail, and, to assess its validity, 3-D QSAutogrid/R has been applied to three molecular data sets of which either CoMFA or GRID/GOLPE models were reported in order to compare the results. 3-D QSAutogrid/R has been used as the core engine to prepare more that 240 3-D QSAR models forming the very first 3-D QSAR server ( www.3d-qsar.com ) with its code freely available through R-Cran distribution.

Place, publisher, year, edition, pages
American Chemical Society (ACS), 2012. Vol. 52, no 6, 1674-85 p.
Keyword [en]
3D QSAR, 3-D QSAutogrid/R, Ligand Based Drug Design, Structure Based Drug Design, Computational Chemistry, Molecular Docking
National Category
Chemical Sciences Computer and Information Science Medicinal Chemistry
Research subject
Medicinal Chemistry; Bioinformatics; Computer Science
Identifiers
URN: urn:nbn:se:uu:diva-321308DOI: 10.1021/ci300123xPubMedID: 22643034OAI: oai:DiVA.org:uu-321308DiVA: diva2:1094665
Available from: 2017-05-10 Created: 2017-05-10 Last updated: 2017-05-12

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