ChemSAR: an online pipelining platform for molecular SAR modeling

Journal of Cheminformatics
Jie DongDong-Sheng Cao

Abstract

In recent years, predictive models based on machine learning techniques have proven to be feasible and effective in drug discovery. However, to develop such a model, researchers usually have to combine multiple tools and undergo several different steps (e.g., RDKit or ChemoPy package for molecular descriptor calculation, ChemAxon Standardizer for structure preprocessing, scikit-learn package for model building, and ggplot2 package for statistical analysis and visualization, etc.). In addition, it may require strong programming skills to accomplish these jobs, which poses severe challenges for users without advanced training in computer programming. Therefore, an online pipelining platform that integrates a number of selected tools is a valuable and efficient solution that can meet the needs of related researchers. This work presents a web-based pipelining platform, called ChemSAR, for generating SAR classification models of small molecules. The capabilities of ChemSAR include the validation and standardization of chemical structure representation, the computation of 783 1D/2D molecular descriptors and ten types of widely-used fingerprints for small molecules, the filtering methods for feature selection, the generation of predic...Continue Reading

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Citations

Mar 19, 2020·Briefings in Bioinformatics·Natesh SinghBruno O Villoutreix
Feb 9, 2020·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Stephani Joy Y MacalinoMaria Constancia O Carrillo
Oct 15, 2019·Database : the Journal of Biological Databases and Curation·Zhihong LiuLiwei Xie
Apr 5, 2019·Journal of Cheminformatics·Kristijan VukovicEmilio Benfenati
Jan 13, 2021·Journal of Cheminformatics·Nalini SchaduangratChanin Nantasenamat
May 16, 2021·International Journal of Pharmaceutics·Jie DongDefang Ouyang
Jul 24, 2021·Seminars in Cancer Biology·Gaspar P PintoDavid Bednar
Aug 21, 2019·Journal of Chemical Information and Modeling·Zi-Yi YangDong-Sheng Cao
Sep 3, 2021·Computational and Structural Biotechnology Journal·Paula Carracedo-ReboredoCarlos Fernandez-Lozano
Oct 21, 2021·Applied Biochemistry and Biotechnology·Priyanka Ramesh, Shanthi Veerappapillai

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Software Mentioned

PaDEL
scikit
QSAR4U
Microsoft windows
OECD QSAR Toolbox
BioTriangle
libSVM
Vcclab
Molecular Operating Environment ( MOE )
PLSR

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