Chemically Aware Model Builder (camb): an R package for property and bioactivity modelling of small molecules

Journal of Cheminformatics
Daniel S MurrellRobert C Glen

Abstract

In silico predictive models have proved to be valuable for the optimisation of compound potency, selectivity and safety profiles in the drug discovery process. camb is an R package that provides an environment for the rapid generation of quantitative Structure-Property and Structure-Activity models for small molecules (including QSAR, QSPR, QSAM, PCM) and is aimed at both advanced and beginner R users. camb's capabilities include the standardisation of chemical structure representation, computation of 905 one-dimensional and 14 fingerprint type descriptors for small molecules, 8 types of amino acid descriptors, 13 whole protein sequence descriptors, filtering methods for feature selection, generation of predictive models (using an interface to the R package caret), as well as techniques to create model ensembles using techniques from the R package caretEnsemble). Results can be visualised through high-quality, customisable plots (R package ggplot2). Overall, camb constitutes an open-source framework to perform the following steps: (1) compound standardisation, (2) molecular and protein descriptor calculation, (3) descriptor pre-processing and model training, visualisation and validation, and (4) bioactivity/property prediction ...Continue Reading

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Citations

Dec 2, 2015·Journal of Chemical Information and Modeling·Isidro Cortes-Ciriano, Andreas Bender
Sep 10, 2015·Bioinformatics·Isidro Cortés-CirianoThérèse E Malliavin
Feb 24, 2015·Journal of Cheminformatics·Isidro Cortes-CirianoThérèse E Malliavin
Jul 12, 2016·Journal of Chemical Information and Modeling·Isidro Cortes-Ciriano
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Dec 17, 2016·Journal of Chemical Information and Modeling·Nicolas BoscPascal Bonnet
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Nov 1, 2017·Journal of Cheminformatics·Jie DongDong-Sheng Cao
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Jun 2, 2018·Journal of Immunology Research·Zidan JinBai Li
Jan 13, 2021·Journal of Cheminformatics·Nalini SchaduangratChanin Nantasenamat
Oct 6, 2016·Molecular Pharmaceutics·Qurrat U AinAndreas Bender
Jun 4, 2015·Journal of Chemical Information and Modeling·Isidro Cortes-CirianoThérèse E Malliavin
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Aug 21, 2018·Journal of Chemical Information and Modeling·Kathryn A GiblinAndreas Bender

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Methods Mentioned

BETA
PCA

Software Mentioned

caret
CorrelationPlot
R package camb : A ware M odel B uilder
ChEMBL
rcdk
Indigo API
- Descriptor
Descriptor Java
PubChem
RDkit

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