Publications by authors named "John W Davies"

35 Publications

Do agricultural grasses bred for improved root systems provide resilience to machinery-derived soil compaction?

Food Energy Secur 2020 Aug 5;9(3):e227. Epub 2020 Jul 5.

Institute of Biological, Environmental and Rural Sciences (IBERS) Aberystwyth University Wales UK.

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August 2020

A multi-scale convolutional neural network for phenotyping high-content cellular images.

Bioinformatics 2017 Jul;33(13):2010-2019

Novartis Institutes for BioMedical Research Inc., Basel, Switzerland.

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July 2017

The opportunities of mining historical and collective data in drug discovery.

Drug Discov Today 2015 Apr 18;20(4):422-34. Epub 2014 Nov 18.

In Silico Lead Discovery, Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge, MA 02139, USA. Electronic address:

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April 2015

Effects of chicory/perennial ryegrass swards compared with perennial ryegrass swards on the performance and carcass quality of grazing beef steers.

PLoS One 2014 28;9(1):e86259. Epub 2014 Jan 28.

Animal and Microbial Sciences, Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Gogerddan, Ceredigion, United Kingdom.

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December 2014

Rethinking molecular similarity: comparing compounds on the basis of biological activity.

ACS Chem Biol 2012 Aug 31;7(8):1399-409. Epub 2012 May 31.

Center for Proteomic Chemistry, Novartis Institutes for Biomedical Research Inc., 250 Massachusetts Avenue, Cambridge, MA 02139, USA.

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August 2012

Chemotography for multi-target SAR analysis in the context of biological pathways.

Bioorg Med Chem 2012 Sep 20;20(18):5416-27. Epub 2012 Feb 20.

Lead Discovery Informatics, Novartis Institutes for Biomedical Research, 250 Massachusetts Ave., Cambridge, MA 02139, USA.

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September 2012

A lead discovery strategy driven by a comprehensive analysis of proteases in the peptide substrate space.

Protein Sci 2010 Nov;19(11):2096-109

Lead Discovery Informatics, Lead Finding Platform, Novartis Institutes for BioMedical Research, Inc., 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA.

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November 2010

Plate-based diversity selection based on empirical HTS data to enhance the number of hits and their chemical diversity.

J Biomol Screen 2009 Jul 16;14(6):690-9. Epub 2009 Jun 16.

Lead Discovery Informatics, Center for Proteomic Chemistry Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, USA.

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July 2009

Gaining insight into off-target mediated effects of drug candidates with a comprehensive systems chemical biology analysis.

J Chem Inf Model 2009 Feb;49(2):308-17

Lead Discovery Informatics and Preclinical Safety Profiling, CPC, Novartis Institutes for Biomedical Research, 250 Massachussetts Avenue, Cambridge, Massachusetts 02139, USA.

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February 2009

Mapping adverse drug reactions in chemical space.

J Med Chem 2009 May;52(9):3103-7

Lead Discovery Informatics, CPC, Novartis Institutes for Biomedical Research, 250 Massachussetts Avenue, Cambridge, Massachusetts 02139, USA.

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May 2009

Use of ligand based models for protein domains to predict novel molecular targets and applications to triage affinity chromatography data.

J Proteome Res 2009 May;8(5):2575-85

Center for Proteomic Chemistry, Lead Discovery Informatics, Developmental and Molecular Pathways, and Global Discovery Chemistry, Chemogenetics and Proteomics, Novartis Institutes for BioMedical Research, Inc., Cambridge, Massachusetts 02139, USA.

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May 2009

How similar are similarity searching methods? A principal component analysis of molecular descriptor space.

J Chem Inf Model 2009 Jan;49(1):108-19

Center for Proteomic Chemistry, Lead Discovery Informatics, Novartis Institutes for BioMedical Research Inc., 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA.

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January 2009

"Virtual fragment linking": an approach to identify potent binders from low affinity fragment hits.

J Med Chem 2008 Apr 22;51(8):2481-91. Epub 2008 Mar 22.

Center for Proteomic Chemistry, Novartis Institutes for BioMedical Research, Inc., 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA.

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April 2008

Entangled palladium nanoparticles in resin plugs.

Chem Commun (Camb) 2007 Dec 4(47):5031-3. Epub 2007 Oct 4.

School of Chemistry, The University of Edinburgh, The King's Buildings, West Mains Road, Edinburgh, UK EH9 3JJ.

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December 2007

Chemogenomic data analysis: prediction of small-molecule targets and the advent of biological fingerprint.

Comb Chem High Throughput Screen 2007 Sep;10(8):719-31

Lead Discovery Informatics, Novartis Institutes for BioMedical Research Inc., 250 Massachusetts Ave., Cambridge, MA 02139, USA.

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September 2007

Understanding false positives in reporter gene assays: in silico chemogenomics approaches to prioritize cell-based HTS data.

J Chem Inf Model 2007 Jul-Aug;47(4):1319-27. Epub 2007 Jul 4.

Lead Discovery Center, Novartis Institutes for Biomedical Research Inc., 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA.

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October 2007

Analysis of pharmacology data and the prediction of adverse drug reactions and off-target effects from chemical structure.

ChemMedChem 2007 Jun;2(6):861-73

Lead Finding Platform, Novartis Institutes for BioMedical Research Inc. 250 Massachusetts Ave., Cambridge, Massachusetts 02139, USA.

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June 2007

Flexible 3D pharmacophores as descriptors of dynamic biological space.

J Mol Graph Model 2007 Oct 1;26(3):622-33. Epub 2007 Mar 1.

Lead Discovery Informatics, Lead Discovery Center, Novartis Institutes for BioMedical Research Inc., 250 Massachusetts Ave., Cambridge, MA 02139, United States.

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October 2007

Bridging chemical and biological space: "target fishing" using 2D and 3D molecular descriptors.

J Med Chem 2006 Nov;49(23):6802-10

Lead Discovery Informatics, Lead Discovery Center, Novartis Institutes for BioMedical Research Inc., 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA.

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November 2006

"Bayes affinity fingerprints" improve retrieval rates in virtual screening and define orthogonal bioactivity space: when are multitarget drugs a feasible concept?

J Chem Inf Model 2006 Nov-Dec;46(6):2445-56

Lead Discovery Informatics, Lead Discovery Center, Novartis Institutes for BioMedical Research Inc., 250 Massachusetts Ave., Cambridge, Massachusetts 02139, USA.

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February 2007

Streamlining lead discovery by aligning in silico and high-throughput screening.

Curr Opin Chem Biol 2006 Aug 5;10(4):343-51. Epub 2006 Jul 5.

Lead Discovery Center, Novartis Institutes for Biomedical Research Inc, 250 Massachusetts Avenue, Cambridge, MA 02139, USA.

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August 2006

Prediction of biological targets for compounds using multiple-category Bayesian models trained on chemogenomics databases.

J Chem Inf Model 2006 May-Jun;46(3):1124-33

Indiana University-Purdue University Indianapolis, School of Informatics, Indianapolis, Indiana 46202, USA.

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June 2006

A 3D similarity method for scaffold hopping from known drugs or natural ligands to new chemotypes.

J Med Chem 2004 Dec;47(25):6144-59

Lead Discovery Center, Novartis Institutes for BioMedical Research Inc., Cambridge, Massachusetts 02139, USA.

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December 2004

Application of machine learning to improve the results of high-throughput docking against the HIV-1 protease.

J Chem Inf Comput Sci 2004 Nov-Dec;44(6):2216-24

Lead Discovery Center, Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA.

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November 2005

Combination of a naive Bayes classifier with consensus scoring improves enrichment of high-throughput docking results.

J Med Chem 2004 Aug;47(18):4356-9

Novartis Institute for Biomedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA.

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August 2004

Finding more needles in the haystack: A simple and efficient method for improving high-throughput docking results.

J Med Chem 2004 May;47(11):2743-9

Novartis Institute for Biomedical Research, 100 Technology Square, Cambridge, Massachusetts 02139, USA.

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May 2004