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

BACKGROUND: In silico predictive models have proved to be valuable for the optimisation of compound potency, selectivity and safety profiles in the drug discovery process. RESULTS: camb is an R package that provides an environment for the rapid generation of quantitative Structure-Property and Struc...

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Autores principales: Murrell, Daniel S, Cortes-Ciriano, Isidro, van Westen, Gerard J P, Stott, Ian P, Bender, Andreas, Malliavin, Thérèse E, Glen, Robert C
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Springer International Publishing 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4551546/
https://www.ncbi.nlm.nih.gov/pubmed/26322135
http://dx.doi.org/10.1186/s13321-015-0086-2
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author Murrell, Daniel S
Cortes-Ciriano, Isidro
van Westen, Gerard J P
Stott, Ian P
Bender, Andreas
Malliavin, Thérèse E
Glen, Robert C
author_facet Murrell, Daniel S
Cortes-Ciriano, Isidro
van Westen, Gerard J P
Stott, Ian P
Bender, Andreas
Malliavin, Thérèse E
Glen, Robert C
author_sort Murrell, Daniel S
collection PubMed
description BACKGROUND: In silico predictive models have proved to be valuable for the optimisation of compound potency, selectivity and safety profiles in the drug discovery process. RESULTS: 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). CONCLUSIONS: 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 for new molecules. camb aims to speed model generation, in order to provide reproducibility and tests of robustness. QSPR and proteochemometric case studies are included which demonstrate camb's application. [Figure: see text] ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13321-015-0086-2) contains supplementary material, which is available to authorized users.
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spelling pubmed-45515462015-08-29 Chemically Aware Model Builder (camb): an R package for property and bioactivity modelling of small molecules Murrell, Daniel S Cortes-Ciriano, Isidro van Westen, Gerard J P Stott, Ian P Bender, Andreas Malliavin, Thérèse E Glen, Robert C J Cheminform Software BACKGROUND: In silico predictive models have proved to be valuable for the optimisation of compound potency, selectivity and safety profiles in the drug discovery process. RESULTS: 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). CONCLUSIONS: 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 for new molecules. camb aims to speed model generation, in order to provide reproducibility and tests of robustness. QSPR and proteochemometric case studies are included which demonstrate camb's application. [Figure: see text] ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13321-015-0086-2) contains supplementary material, which is available to authorized users. Springer International Publishing 2015-08-28 /pmc/articles/PMC4551546/ /pubmed/26322135 http://dx.doi.org/10.1186/s13321-015-0086-2 Text en © Murrell et al. 2015 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Software
Murrell, Daniel S
Cortes-Ciriano, Isidro
van Westen, Gerard J P
Stott, Ian P
Bender, Andreas
Malliavin, Thérèse E
Glen, Robert C
Chemically Aware Model Builder (camb): an R package for property and bioactivity modelling of small molecules
title Chemically Aware Model Builder (camb): an R package for property and bioactivity modelling of small molecules
title_full Chemically Aware Model Builder (camb): an R package for property and bioactivity modelling of small molecules
title_fullStr Chemically Aware Model Builder (camb): an R package for property and bioactivity modelling of small molecules
title_full_unstemmed Chemically Aware Model Builder (camb): an R package for property and bioactivity modelling of small molecules
title_short Chemically Aware Model Builder (camb): an R package for property and bioactivity modelling of small molecules
title_sort chemically aware model builder (camb): an r package for property and bioactivity modelling of small molecules
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4551546/
https://www.ncbi.nlm.nih.gov/pubmed/26322135
http://dx.doi.org/10.1186/s13321-015-0086-2
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