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XenoSite specifications

Information


Unique identifier OMICS_07587
Name XenoSite
Alternative name XenoSite-Region
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline S. Joshua Swamidass

Information


Unique identifier OMICS_07587
Name XenoSite
Alternative name XenoSite-Region
Interface Web user interface
Restrictions to use None
Input data Some molecular structures.
Input format Smiles,SDF
Programming languages Python
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline S. Joshua Swamidass

Publications for XenoSite

XenoSite citations

 (4)
library_books

Predicting the Metabolic Sites by Flavin Containing Monooxygenase on Drug Molecules Using SVM Classification on Computed Quantum Mechanics and Circular Fingerprints Molecular Descriptors

2017
PLoS One
PMCID: 5224990
PMID: 28072829
DOI: 10.1371/journal.pone.0169910

[…] topological and 392 quantum mechanics atomic descriptors including contributions from neighbouring atoms.There are other machine learning approaches using different descriptors to predict SOM such as Xenosite [] using the Daylight fingerprint descriptors []. A SVM method [] using the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database [] and other various descriptors has been published […]

library_books

Modeling Reactivity to Biological Macromolecules with a Deep Multitask Network

2016
PMCID: 4999971
PMID: 27610414
DOI: 10.1021/acscentsci.6b00162

[…] , such as each molecule’s connectivity distance matrix, periodic table properties, or motif patterns defined by Pybel. The majority of our topological descriptors have been shown to be useful for the XenoSite metabolism, reactivity, and epoxidation models.,, In this study, we used an expanded set of topological descriptors, which slightly improved performance in comparison to the previous set of t […]

library_books

Modeling Epoxidation of Drug like Molecules with a Deep Machine Learning Network

2015
PMCID: 4827534
PMID: 27162970
DOI: 10.1021/acscentsci.5b00131

[…] -house software that took as input SDF files with explicit hydrogens and 3D coordinates created by Open Babel. The majority of our descriptors were atom-level descriptors previously developed for the XenoSite metabolism model and the XenoSite reactivity model. Each bond contained 89 descriptors from its “left” atom and its “right” atom. To prevent representation bias due to atom ordering, left and […]

library_books

Cytochrome P450 site of metabolism prediction from 2D topological fingerprints using GPU accelerated probabilistic classifiers

2014
J Cheminform
PMCID: 4047555
PMID: 24959208
DOI: 10.1186/1758-2946-6-29

[…] t SoM using 148 topological and 392 quantum chemical atomic descriptors where some of these descriptors are modified to include contributions from neighbouring atoms. A neural network approach called Xenosite [] has also been applied to this descriptor set but combined with other molecular descriptors and fingerprint descriptors based on the Daylight [] definition. A probability score that each at […]

Citations

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XenoSite institution(s)
Division of Biology and Biological Sciences Washington University School of Medicine, St. Louis, MO, USA; Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
XenoSite funding source(s)
Supported by the Pathology and Immunology Department of Washington University in Saint Louis.

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a convenient and fast tool to understand potential toxicophores