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Validating the validation: reanalyzing a large-scale comparison of deep learning and machine learning models for bioactivity prediction.

Robinson MC, Glen RC, Lee AA.

J Comput Aided Mol Des. 2020 Jan 20. doi: 10.1007/s10822-019-00274-0. [Epub ahead of print]


A Bone Morphogenetic Protein (BMP)-derived Peptide Based on the Type I Receptor-binding Site Modifies Cell-type Dependent BMP Signalling.

Tong Z, Guo J, Glen RC, Morrell NW, Li W.

Sci Rep. 2019 Sep 17;9(1):13446. doi: 10.1038/s41598-019-49758-x.


International Union of Basic and Clinical Pharmacology. CVII. Structure and Pharmacology of the Apelin Receptor with a Recommendation that Elabela/Toddler Is a Second Endogenous Peptide Ligand.

Read C, Nyimanu D, Williams TL, Huggins DJ, Sulentic P, Macrae RGC, Yang P, Glen RC, Maguire JJ, Davenport AP.

Pharmacol Rev. 2019 Oct;71(4):467-502. doi: 10.1124/pr.119.017533. Review.


The structural basis for membrane assembly of immunoreceptor signalling complexes.

Dube N, Marzinek JK, Glen RC, Bond PJ.

J Mol Model. 2019 Aug 27;25(9):277. doi: 10.1007/s00894-019-4165-6.


The nPYc-Toolbox, a Python module for the pre-processing, quality-control and analysis of metabolic profiling datasets.

Sands CJ, Wolfer AM, Correia GDS, Sadawi N, Ahmed A, Jiménez B, Lewis MR, Glen RC, Nicholson JK, Pearce JTM.

Bioinformatics. 2019 Dec 15;35(24):5359-5360. doi: 10.1093/bioinformatics/btz566.


Colocalization Features for Classification of Tumors Using Desorption Electrospray Ionization Mass Spectrometry Imaging.

Inglese P, Correia G, Pruski P, Glen RC, Takats Z.

Anal Chem. 2019 May 21;91(10):6530-6540. doi: 10.1021/acs.analchem.8b05598. Epub 2019 May 1.


Apelin peptides linked to anti-serum albumin domain antibodies retain affinity in vitro and are efficacious receptor agonists in vivo.

Read C, Yang P, Kuc RE, Nyimanu D, Williams TL, Glen RC, Holt LJ, Arulanantham H, Smart A, Davenport AP, Maguire JJ.

Basic Clin Pharmacol Toxicol. 2019 Mar 22. doi: 10.1111/bcpt.13227. [Epub ahead of print]


A novel cyclic biased agonist of the apelin receptor, MM07, is disease modifying in the rat monocrotaline model of pulmonary arterial hypertension.

Yang P, Read C, Kuc RE, Nyimanu D, Williams TL, Crosby A, Buonincontri G, Southwood M, Sawiak SJ, Glen RC, Morrell NW, Davenport AP, Maguire JJ.

Br J Pharmacol. 2019 May;176(9):1206-1221. doi: 10.1111/bph.14603. Epub 2019 Apr 1.


Structure-based design of allosteric calpain-1 inhibitors populating a novel bioactivity space.

Kalash L, Cresser-Brown J, Habchi J, Morgan C, Miller DJ, Glen RC, Allemann RK, Bender A.

Eur J Med Chem. 2018 Sep 5;157:1264-1275. doi: 10.1016/j.ejmech.2018.08.049. Epub 2018 Aug 23.


SPUTNIK: an R package for filtering of spatially related peaks in mass spectrometry imaging data.

Inglese P, Correia G, Takats Z, Nicholson JK, Glen RC.

Bioinformatics. 2019 Jan 1;35(1):178-180. doi: 10.1093/bioinformatics/bty622.


Microbiome-host systems interactions: protective effects of propionate upon the blood-brain barrier.

Hoyles L, Snelling T, Umlai UK, Nicholson JK, Carding SR, Glen RC, McArthur S.

Microbiome. 2018 Mar 21;6(1):55. doi: 10.1186/s40168-018-0439-y.


Pharmacological targeting of apelin impairs glioblastoma growth.

Harford-Wright E, Andre-Gregoire G, Jacobs KA, Treps L, Le Gonidec S, Leclair HM, Gonzalez-Diest S, Roux Q, Guillonneau F, Loussouarn D, Oliver L, Vallette FM, Foufelle F, Valet P, Davenport AP, Glen RC, Bidere N, Gavard J.

Brain. 2017 Nov 1;140(11):2939-2954. doi: 10.1093/brain/awx253.


Deep learning and 3D-DESI imaging reveal the hidden metabolic heterogeneity of cancer.

Inglese P, McKenzie JS, Mroz A, Kinross J, Veselkov K, Holmes E, Takats Z, Nicholson JK, Glen RC.

Chem Sci. 2017 May 1;8(5):3500-3511. doi: 10.1039/c6sc03738k. Epub 2017 Feb 21.


[Pyr1]Apelin-13(1-12) Is a Biologically Active ACE2 Metabolite of the Endogenous Cardiovascular Peptide [Pyr1]Apelin-13.

Yang P, Kuc RE, Brame AL, Dyson A, Singer M, Glen RC, Cheriyan J, Wilkinson IB, Davenport AP, Maguire JJ.

Front Neurosci. 2017 Feb 28;11:92. doi: 10.3389/fnins.2017.00092. eCollection 2017.


Elabela/Toddler Is an Endogenous Agonist of the Apelin APJ Receptor in the Adult Cardiovascular System, and Exogenous Administration of the Peptide Compensates for the Downregulation of Its Expression in Pulmonary Arterial Hypertension.

Yang P, Read C, Kuc RE, Buonincontri G, Southwood M, Torella R, Upton PD, Crosby A, Sawiak SJ, Carpenter TA, Glen RC, Morrell NW, Maguire JJ, Davenport AP.

Circulation. 2017 Mar 21;135(12):1160-1173. doi: 10.1161/CIRCULATIONAHA.116.023218. Epub 2017 Jan 30.


Computational tools and workflows in metabolomics: An international survey highlights the opportunity for harmonisation through Galaxy.

Weber RJM, Lawson TN, Salek RM, Ebbels TMD, Glen RC, Goodacre R, Griffin JL, Haug K, Koulman A, Moreno P, Ralser M, Steinbeck C, Dunn WB, Viant MR.

Metabolomics. 2017;13(2):12. doi: 10.1007/s11306-016-1147-x. Epub 2016 Dec 27. No abstract available.


Multiple-parameter Optimization in Drug Discovery: Example of the 5-HT1B GPCR.

Glen RC, Galloway WR, Spring DR, Liwiki G.

Mol Inform. 2016 Dec;35(11-12):599-605. doi: 10.1002/minf.201600056. Epub 2016 Jul 11.


Analysis of Differential Efficacy and Affinity of GABAA (α1/α2) Selective Modulators.

Ain QU, Owen RM, Omoto K, Torella R, Bulusu KC, Pryde DC, Glen RC, Fuchs JE, Bender A.

Mol Pharm. 2016 Nov 7;13(11):4001-4012. Epub 2016 Oct 20.


Cardiac action of the first G protein biased small molecule apelin agonist.

Read C, Fitzpatrick CM, Yang P, Kuc RE, Maguire JJ, Glen RC, Foster RE, Davenport AP.

Biochem Pharmacol. 2016 Sep 15;116:63-72. doi: 10.1016/j.bcp.2016.07.018. Epub 2016 Jul 27.


Improving the prediction of organism-level toxicity through integration of chemical, protein target and cytotoxicity qHTS data.

Allen CHG, Koutsoukas A, Cortés-Ciriano I, Murrell DS, Malliavin TE, Glen RC, Bender A.

Toxicol Res (Camb). 2016 Mar 3;5(3):883-894. doi: 10.1039/c5tx00406c. eCollection 2016 May 1.


A note on utilising binary features as ligand descriptors.

Mussa HY, Mitchell JB, Glen RC.

J Cheminform. 2015 Dec 1;7:58. doi: 10.1186/s13321-015-0105-3. eCollection 2015.


Cheminformatics Research at the Unilever Centre for Molecular Science Informatics Cambridge.

Fuchs JE, Bender A, Glen RC.

Mol Inform. 2015 Sep;34(9):626-633. Epub 2015 Mar 10.


Molecular mechanism of a specific capsid binder resistance caused by mutations outside the binding pocket.

Braun H, Kirchmair J, Williamson MJ, Makarov VA, Riabova OB, Glen RC, Sauerbrei A, Schmidtke M.

Antiviral Res. 2015 Nov;123:138-45. doi: 10.1016/j.antiviral.2015.09.009. Epub 2015 Sep 25.


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

Murrell DS, Cortes-Ciriano I, van Westen GJP, Stott IP, Bender A, Malliavin TE, Glen RC.

J Cheminform. 2015 Aug 28;7:45. doi: 10.1186/s13321-015-0086-2. eCollection 2015.


Metrabase: a cheminformatics and bioinformatics database for small molecule transporter data analysis and (Q)SAR modeling.

Mak L, Marcus D, Howlett A, Yarova G, Duchateau G, Klaffke W, Bender A, Glen RC.

J Cheminform. 2015 Jun 23;7:31. doi: 10.1186/s13321-015-0083-5. eCollection 2015.


Verifying the fully "Laplacianised" posterior Naïve Bayesian approach and more.

Mussa HY, Marcus D, Mitchell JB, Glen RC.

J Cheminform. 2015 Jun 12;7:27. doi: 10.1186/s13321-015-0075-5. eCollection 2015.


A multi-label approach to target prediction taking ligand promiscuity into account.

Afzal AM, Mussa HY, Turner RE, Bender A, Glen RC.

J Cheminform. 2015 May 30;7:24. doi: 10.1186/s13321-015-0071-9. eCollection 2015.


Predicting drug metabolism: experiment and/or computation?

Kirchmair J, Göller AH, Lang D, Kunze J, Testa B, Wilson ID, Glen RC, Schneider G.

Nat Rev Drug Discov. 2015 Jun;14(6):387-404. doi: 10.1038/nrd4581. Epub 2015 Apr 24. Review.


Design, characterization, and first-in-human study of the vascular actions of a novel biased apelin receptor agonist.

Brame AL, Maguire JJ, Yang P, Dyson A, Torella R, Cheriyan J, Singer M, Glen RC, Wilkinson IB, Davenport AP.

Hypertension. 2015 Apr;65(4):834-40. doi: 10.1161/HYPERTENSIONAHA.114.05099. Epub 2015 Feb 23.


Extending in silico mechanism-of-action analysis by annotating targets with pathways: application to cellular cytotoxicity readouts.

Liggi S, Drakakis G, Koutsoukas A, Cortes-Ciriano I, Martínez-Alonso P, Malliavin TE, Velazquez-Campoy A, Brewerton SC, Bodkin MJ, Evans DA, Glen RC, Carrodeguas JA, Bender A.

Future Med Chem. 2014;6(18):2029-56. doi: 10.4155/fmc.14.137.


A combination of computational and experimental approaches identifies DNA sequence constraints associated with target site binding specificity of the transcription factor CSL.

Torella R, Li J, Kinrade E, Cerda-Moya G, Contreras AN, Foy R, Stojnic R, Glen RC, Kovall RA, Adryan B, Bray SJ.

Nucleic Acids Res. 2014;42(16):10550-63. doi: 10.1093/nar/gku730. Epub 2014 Aug 11.


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

Tyzack JD, Mussa HY, Williamson MJ, Kirchmair J, Glen RC.

J Cheminform. 2014 May 27;6:29. doi: 10.1186/1758-2946-6-29. eCollection 2014.


Investigating and Predicting how Biology Changes Molecules and Their Properties.

Tyzack JD, Glen RC.

Mol Inform. 2014 Jun;33(6-7):443-5. doi: 10.1002/minf.201400031. Epub 2014 May 13.


How diverse are diversity assessment methods? A comparative analysis and benchmarking of molecular descriptor space.

Koutsoukas A, Paricharak S, Galloway WR, Spring DR, Ijzerman AP, Glen RC, Marcus D, Bender A.

J Chem Inf Model. 2014 Jan 27;54(1):230-42. doi: 10.1021/ci400469u. Epub 2013 Dec 13.


FAst MEtabolizer (FAME): A rapid and accurate predictor of sites of metabolism in multiple species by endogenous enzymes.

Kirchmair J, Williamson MJ, Afzal AM, Tyzack JD, Choy AP, Howlett A, Rydberg P, Glen RC.

J Chem Inf Model. 2013 Nov 25;53(11):2896-907. doi: 10.1021/ci400503s. Epub 2013 Nov 12.


Full "Laplacianised" posterior naive Bayesian algorithm.

Mussa HY, Mitchell JB, Glen RC.

J Cheminform. 2013 Aug 23;5(1):37. doi: 10.1186/1758-2946-5-37.


Linking Ayurveda and Western medicine by integrative analysis.

Fauzi FM, Koutsoukas A, Lowe R, Joshi K, Fan TP, Glen RC, Bender A.

J Ayurveda Integr Med. 2013 Apr;4(2):117-9. doi: 10.4103/0975-9476.113882.


In silico target predictions: defining a benchmarking data set and comparison of performance of the multiclass Naïve Bayes and Parzen-Rosenblatt window.

Koutsoukas A, Lowe R, Kalantarmotamedi Y, Mussa HY, Klaffke W, Mitchell JB, Glen RC, Bender A.

J Chem Inf Model. 2013 Aug 26;53(8):1957-66. doi: 10.1021/ci300435j. Epub 2013 Jul 24. Erratum in: J Chem Inf Model. 2014 Jul 28;54(7):2180-2.


Prediction of cytochrome P450 xenobiotic metabolism: tethered docking and reactivity derived from ligand molecular orbital analysis.

Tyzack JD, Williamson MJ, Torella R, Glen RC.

J Chem Inf Model. 2013 Jun 24;53(6):1294-305. doi: 10.1021/ci400058s. Epub 2013 May 24.


Diversity selection of compounds based on 'protein affinity fingerprints' improves sampling of bioactive chemical space.

Nguyen HP, Koutsoukas A, Mohd Fauzi F, Drakakis G, Maciejewski M, Glen RC, Bender A.

Chem Biol Drug Des. 2013 Sep;82(3):252-66. doi: 10.1111/cbdd.12155.


Chemogenomics approaches to rationalizing the mode-of-action of traditional Chinese and Ayurvedic medicines.

Mohd Fauzi F, Koutsoukas A, Lowe R, Joshi K, Fan TP, Glen RC, Bender A.

J Chem Inf Model. 2013 Mar 25;53(3):661-73. doi: 10.1021/ci3005513. Epub 2013 Feb 18.


How do metabolites differ from their parent molecules and how are they excreted?

Kirchmair J, Howlett A, Peironcely JE, Murrell DS, Williamson MJ, Adams SE, Hankemeier T, van Buren L, Duchateau G, Klaffke W, Glen RC.

J Chem Inf Model. 2013 Feb 25;53(2):354-67. doi: 10.1021/ci300487z. Epub 2013 Jan 25.


Anti-cancer drug development: computational strategies to identify and target proteins involved in cancer metabolism.

Mak L, Liggi S, Tan L, Kusonmano K, Rollinger JM, Koutsoukas A, Glen RC, Kirchmair J.

Curr Pharm Des. 2013;19(4):532-77. Review.


Probability Based hERG Blocker Classifiers.

Wang Z, Mussa HY, Lowe R, Glen RC, Yan A.

Mol Inform. 2012 Sep;31(9):679-85. doi: 10.1002/minf.201200011. Epub 2012 Sep 7.


Note on naive Bayes based on binary descriptors in cheminformatics.

Townsend JA, Glen RC, Mussa HY.

J Chem Inf Model. 2012 Oct 22;52(10):2494-500. doi: 10.1021/ci200303m. Epub 2012 Sep 17.


Computational prediction of metabolism: sites, products, SAR, P450 enzyme dynamics, and mechanisms.

Kirchmair J, Williamson MJ, Tyzack JD, Tan L, Bond PJ, Bender A, Glen RC.

J Chem Inf Model. 2012 Mar 26;52(3):617-48. doi: 10.1021/ci200542m. Epub 2012 Feb 17. Review.


The challenges involved in modeling toxicity data in silico: a review.

Gleeson MP, Modi S, Bender A, Robinson RL, Kirchmair J, Promkatkaew M, Hannongbua S, Glen RC.

Curr Pharm Des. 2012;18(9):1266-91. Review.


Predicting the mechanism of phospholipidosis.

Lowe R, Mussa HY, Nigsch F, Glen RC, Mitchell JB.

J Cheminform. 2012 Jan 26;4:2. doi: 10.1186/1758-2946-4-2.


Computational chemistry and cheminformatics: an essay on the future.

Glen RC.

J Comput Aided Mol Des. 2012 Jan;26(1):47-9. doi: 10.1007/s10822-011-9501-6. Epub 2011 Dec 13.


Classifying molecules using a sparse probabilistic kernel binary classifier.

Lowe R, Mussa HY, Mitchell JB, Glen RC.

J Chem Inf Model. 2011 Jul 25;51(7):1539-44. doi: 10.1021/ci200128w. Epub 2011 Jul 8.


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