Andreas Bender

Centre for Molecular Informatics, University of Cambridge

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JoVE Journal Publications

ArticleTotal : 1	Year
Publication title Cited by 3	2018

Other Publications

Article	Year
Molecular similarity searching using atom environments, information-based feature selection, and a naïve Bayesian classifier. Journal of chemical information and computer sciences\| PubMed ID: 14741025	2004
Similarity searching of chemical databases using atom environment descriptors (MOLPRINT 2D): evaluation of performance. Journal of chemical information and computer sciences\| PubMed ID: 15446830	2004
Molecular similarity: a key technique in molecular informatics. Organic & biomolecular chemistry\| PubMed ID: 15534697	2004
Molecular surface point environments for virtual screening and the elucidation of binding patterns (MOLPRINT 3D). Journal of medicinal chemistry\| PubMed ID: 15588092	2004
Assessment of structural diversity in combinatorial synthesis. Current opinion in chemical biology\| PubMed ID: 15939333	2005
Screening for dihydrofolate reductase inhibitors using MOLPRINT 2D, a fast fragment-based method employing the naïve Bayesian classifier: limitations of the descriptor and the importance of ... Journal of biomolecular screening\| PubMed ID: 16170051	2005
A discussion of measures of enrichment in virtual screening: comparing the information content of descriptors with increasing levels of sophistication. Journal of chemical information and modeling\| PubMed ID: 16180913	2005
Circular fingerprints: flexible molecular descriptors with applications from physical chemistry to ADME. IDrugs : the investigational drugs journal\| PubMed ID: 16523386	2006
Diversity oriented synthesis: a challenge for synthetic chemists. Ernst Schering Research Foundation workshop\| PubMed ID: 16708998	2006
Skeletal diversity construction via a branching synthetic strategy. Chemical communications (Cambridge, England)\| PubMed ID: 16883415	2006
Chemoinformatics-based classification of prohibited substances employed for doping in sport. Journal of chemical information and modeling\| PubMed ID: 17125180	2006
Melting point prediction employing k-nearest neighbor algorithms and genetic parameter optimization. Journal of chemical information and modeling\| PubMed ID: 17125183	2006
Support vector inductive logic programming outperforms the naive Bayes classifier and inductive logic programming for the classification of bioactive chemical compounds. Journal of computer-aided molecular design\| PubMed ID: 17387437	2007
Anti-MRSA agent discovery using diversity-oriented synthesis. Angewandte Chemie (International ed. in English)\| PubMed ID: 18307176	2008
Diversity-oriented synthesis; a spectrum of approaches and results. Organic & biomolecular chemistry\| PubMed ID: 18362950	2008
Ligand-target prediction using Winnow and naive Bayesian algorithms and the implications of overall performance statistics. Journal of chemical information and modeling\| PubMed ID: 19055411	2008
The discovery of antibacterial agents using diversity-oriented synthesis. Chemical communications (Cambridge, England)\| PubMed ID: 19532856	2009
Dynamic clustering threshold reduces conformer ensemble size while maintaining a biologically relevant ensemble. Journal of computer-aided molecular design\| PubMed ID: 20499135	2010
A novel chemogenomics analysis of G protein-coupled receptors (GPCRs) and their ligands: a potential strategy for receptor de-orphanization. BMC bioinformatics\| PubMed ID: 20537162	2010
Increased diversity of libraries from libraries: chemoinformatic analysis of bis-diazacyclic libraries. Chemical biology & drug design\| PubMed ID: 21294850	2011
Diversity-oriented synthesis of macrocyclic peptidomimetics. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 21383137	2011
From in silico target prediction to multi-target drug design: current databases, methods and applications. Journal of proteomics\| PubMed ID: 21621023	2011
Online chemical modeling environment (OCHEM): web platform for data storage, model development and publishing of chemical information. Journal of computer-aided molecular design\| PubMed ID: 21660515	2011
Which compound to select in lead optimization? Prospectively validated proteochemometric models guide preclinical development. PloS one\| PubMed ID: 22132107	2011
Understanding and classifying metabolite space and metabolite-likeness. PloS one\| PubMed ID: 22194963	2011
Computational prediction of metabolism: sites, products, SAR, P450 enzyme dynamics, and mechanisms. Journal of chemical information and modeling\| PubMed ID: 22339582	2012
How similar are those molecules after all? Use two descriptors and you will have three different answers. Expert opinion on drug discovery\| PubMed ID: 22822717	2010
A two-directional strategy for the diversity-oriented synthesis of macrocyclic scaffolds. Organic & biomolecular chemistry\| PubMed ID: 22890306	2012
Chemogenomics approaches to rationalizing the mode-of-action of traditional Chinese and Ayurvedic medicines. Journal of chemical information and modeling\| PubMed ID: 23351136	2013
Significantly improved HIV inhibitor efficacy prediction employing proteochemometric models generated from antivirogram data. PLoS computational biology\| PubMed ID: 23436985	2013
Diversity selection of compounds based on 'protein affinity fingerprints' improves sampling of bioactive chemical space. Chemical biology & drug design\| PubMed ID: 23647865	2013
In silico target predictions: defining a benchmarking data set and comparison of performance of the multiclass Naïve Bayes and Parzen-Rosenblatt window. Journal of chemical information and modeling\| PubMed ID: 23829430	2013
Computer-aided (in silico) approaches in the mode-of-action analysis and safety assessment of ostarine and 4-methylamphetamine. Human psychopharmacology\| PubMed ID: 23881885	2013
Linking Ayurveda and Western medicine by integrative analysis. Journal of Ayurveda and integrative medicine\| PubMed ID: 23930045	2013
Benchmarking of protein descriptor sets in proteochemometric modeling (part 1): comparative study of 13 amino acid descriptor sets. Journal of cheminformatics\| PubMed ID: 24059694	2013
Benchmarking of protein descriptor sets in proteochemometric modeling (part 2): modeling performance of 13 amino acid descriptor sets. Journal of cheminformatics\| PubMed ID: 24059743	2013
Design, synthesis, and biological evaluation of an allosteric inhibitor of HSET that targets cancer cells with supernumerary centrosomes. Chemistry & biology\| PubMed ID: 24210220	2013
How diverse are diversity assessment methods? A comparative analysis and benchmarking of molecular descriptor space. Journal of chemical information and modeling\| PubMed ID: 24289493	2014
Are phylogenetic trees suitable for chemogenomics analyses of bioactivity data sets: the importance of shared active compounds and choosing a suitable data embedding method, as exemplified o... Journal of cheminformatics\| PubMed ID: 24330772	2013
A-ring dihalogenation increases the cellular activity of combretastatin-templated tetrazoles. ACS medicinal chemistry letters\| PubMed ID: 24900453	2012
Proteochemometric modeling in a Bayesian framework. Journal of cheminformatics\| PubMed ID: 25045403	2014
Novel benzoxazine-based aglycones block glucose uptake in vivo by inhibiting glycosidases. PloS one\| PubMed ID: 25047583	2014
Novel synthetic biscoumarins target tumor necrosis factor-α in hepatocellular carcinoma in vitro and in vivo. The Journal of biological chemistry\| PubMed ID: 25231984	2014
Connecting gene expression data from connectivity map and in silico target predictions for small molecule mechanism-of-action analysis. Molecular bioSystems\| PubMed ID: 25254964	2015
Modelling ligand selectivity of serine proteases using integrative proteochemometric approaches improves model performance and allows the multi-target dependent interpretation of features. Integrative biology : quantitative biosciences from nano to macro\| PubMed ID: 25255469	2014
Synthesis and characterization of novel 2-amino-chromene-nitriles that target Bcl-2 in acute myeloid leukemia cell lines. PloS one\| PubMed ID: 25268519	2014
Development of a novel azaspirane that targets the Janus kinase-signal transducer and activator of transcription (STAT) pathway in hepatocellular carcinoma in vitro and in vivo. The Journal of biological chemistry\| PubMed ID: 25320076	2014
Towards predictive resistance models for agrochemicals by combining chemical and protein similarity via proteochemometric modelling. Journal of chemical biology\| PubMed ID: 25320644	2014
Extending in silico mechanism-of-action analysis by annotating targets with pathways: application to cellular cytotoxicity readouts. Future medicinal chemistry\| PubMed ID: 25531967	2014
Using transcriptomics to guide lead optimization in drug discovery projects: Lessons learned from the QSTAR project. Drug discovery today\| PubMed ID: 25582842	2015
Novel synthetic coumarins that targets NF-κB in Hepatocellular carcinoma. Bioorganic & medicinal chemistry letters\| PubMed ID: 25592709	2015
Analyzing multitarget activity landscapes using protein-ligand interaction fingerprints: interaction cliffs. Journal of chemical information and modeling\| PubMed ID: 25615841	2015
Prediction of the potency of mammalian cyclooxygenase inhibitors with ensemble proteochemometric modeling. Journal of cheminformatics\| PubMed ID: 25705261	2015
Comparing global and local likelihood score thresholds in multiclass laplacian-modified Naive Bayes protein target prediction. Combinatorial chemistry & high throughput screening\| PubMed ID: 25747441	2015
Microwave-assisted synthesis, characterization and cytotoxic studies of novel estrogen receptor α ligands towards human breast cancer cells. Bioorganic & medicinal chemistry letters\| PubMed ID: 25797502	2015
Proteochemometric modelling coupled to in silico target prediction: an integrated approach for the simultaneous prediction of polypharmacology and binding affinity/potency of small molecules... Journal of cheminformatics\| PubMed ID: 25926892	2015
Comparing the Influence of Simulated Experimental Errors on 12 Machine Learning Algorithms in Bioactivity Modeling Using 12 Diverse Data Sets. Journal of chemical information and modeling\| PubMed ID: 26038978	2015
Synthesis and characterization of novel oxazines and demonstration that they specifically target cyclooxygenase 2. Bioorganic & medicinal chemistry letters\| PubMed ID: 26048794	2015
A multi-label approach to target prediction taking ligand promiscuity into account. Journal of cheminformatics\| PubMed ID: 26064191	2015
Metrabase: a cheminformatics and bioinformatics database for small molecule transporter data analysis and (Q)SAR modeling. Journal of cheminformatics\| PubMed ID: 26106450	2015
A One Pot Synthesis of Novel Bioactive Tri-Substitute-Condensed-Imidazopyridines that Targets Snake Venom Phospholipase A2. PloS one\| PubMed ID: 26196520	2015
Design, synthesis and evaluation of semi-synthetic triazole-containing caffeic acid analogues as 5-lipoxygenase inhibitors. European journal of medicinal chemistry\| PubMed ID: 26197161	2015
Synergy Maps: exploring compound combinations using network-based visualization. Journal of cheminformatics\| PubMed ID: 26236402	2015
Synthesis of 1,2-benzisoxazole tethered 1,2,3-triazoles that exhibit anticancer activity in acute myeloid leukemia cell lines by inhibiting histone deacetylases, and inducing p21 and tubulin... Bioorganic & medicinal chemistry\| PubMed ID: 26299825	2015
Chemically Aware Model Builder (camb): an R package for property and bioactivity modelling of small molecules. Journal of cheminformatics\| PubMed ID: 26322135	2015
Synthesis, characterization and in vitro evaluation of novel enantiomerically-pure sulphonamide antimalarials. Organic & biomolecular chemistry\| PubMed ID: 26347024	2015
Improved large-scale prediction of growth inhibition patterns using the NCI60 cancer cell line panel. Bioinformatics (Oxford, England)\| PubMed ID: 26351271	2016
Modelling of compound combination effects and applications to efficacy and toxicity: state-of-the-art, challenges and perspectives. Drug discovery today\| PubMed ID: 26360051	2016
Development of Novel Triazolo-Thiadiazoles from Heterogeneous "Green" Catalysis as Protein Tyrosine Phosphatase 1B Inhibitors. Scientific reports\| PubMed ID: 26388336	2015
Cheminformatics Research at the Unilever Centre for Molecular Science Informatics Cambridge. Molecular informatics\| PubMed ID: 26435758	2015
A Nano-MgO and Ionic Liquid-Catalyzed 'Green' Synthesis Protocol for the Development of Adamantyl-Imidazolo-Thiadiazoles as Anti-Tuberculosis Agents Targeting Sterol 14α-Demethylase (CYP51). PloS one\| PubMed ID: 26470029	2015
Target prediction utilising negative bioactivity data covering large chemical space. Journal of cheminformatics\| PubMed ID: 26500705	2015
How Consistent are Publicly Reported Cytotoxicity Data? Large-Scale Statistical Analysis of the Concordance of Public Independent Cytotoxicity Measurements. ChemMedChem\| PubMed ID: 26541361	2016
Improved Chemical Structure-Activity Modeling Through Data Augmentation. Journal of chemical information and modeling\| PubMed ID: 26619900	2015
ARWAR: A network approach for predicting Adverse Drug Reactions. Computers in biology and medicine\| PubMed ID: 26638149	2016
Adamantyl-tethered-biphenylic compounds induce apoptosis in cancer cells by targeting Bcl homologs. Bioorganic & medicinal chemistry letters\| PubMed ID: 26725030	2016
Analysis of Iterative Screening with Stepwise Compound Selection Based on Novartis In-house HTS Data. ACS chemical biology\| PubMed ID: 26878899	2016
Global Mapping of Traditional Chinese Medicine into Bioactivity Space and Pathways Annotation Improves Mechanistic Understanding and Discovers Relationships between Therapeutic Action (Sub)c... Evidence-based complementary and alternative medicine : eCAM\| PubMed ID: 26989424	2016
Trisubstituted-Imidazoles Induce Apoptosis in Human Breast Cancer Cells by Targeting the Oncogenic PI3K/Akt/mTOR Signaling Pathway. PloS one\| PubMed ID: 27097161	2016
Synthesis and in vitro evaluation of hydrazinyl phthalazines against malaria parasite, Plasmodium falciparum. Bioorganic & medicinal chemistry letters\| PubMed ID: 27261180	2016
Understanding the mode-of-action of Cassia auriculata via in silico and in vivo studies towards validating it as a long term therapy for type II diabetes. Journal of ethnopharmacology\| PubMed ID: 27452659	2017
Virtual Activity Profiling of Bioactive Molecules by 1D Fingerprinting. Molecular informatics\| PubMed ID: 27464267	2010
Extensions to In Silico Bioactivity Predictions Using Pathway Annotations and Differential Pharmacology Analysis: Application to Xenopus laevis Phenotypic Readouts. Molecular informatics\| PubMed ID: 27481146	2013
Data-Driven Derivation of an "Informer Compound Set" for Improved Selection of Active Compounds in High-Throughput Screening. Journal of chemical information and modeling\| PubMed ID: 27487177	2016
Prediction of PARP Inhibition with Proteochemometric Modelling and Conformal Prediction. Molecular informatics\| PubMed ID: 27490382	2015
Understanding Cytotoxicity and Cytostaticity in a High-Throughput Screening Collection. ACS chemical biology\| PubMed ID: 27571164	2016
Simultaneous Prediction of four ATP-binding Cassette Transporters' Substrates Using Multi-label QSAR. Molecular informatics\| PubMed ID: 27582431	2016
Analysis of Differential Efficacy and Affinity of GABA (α1/α2) Selective Modulators. Molecular pharmaceutics\| PubMed ID: 27704838	2016
Data-driven approaches used for compound library design, hit triage and bioactivity modeling in high-throughput screening. Briefings in bioinformatics\| PubMed ID: 27789427	2018
In silico target prediction for elucidating the mode of action of herbicides including prospective validation. Journal of molecular graphics & modelling\| PubMed ID: 27846423	2017
Diversity selection, screening and quantitative structure-activity relationships of osmolyte-like additive effects on the thermal stability of a monoclonal antibody. European journal of pharmaceutical sciences : official journal of the European Federation for Pharmaceutical Sciences\| PubMed ID: 27866015	2017
Fragment Profiling Approach to Inhibitors of the Orphan M. tuberculosis P450 CYP144A1. Biochemistry\| PubMed ID: 28169518	2017
Improving Screening Efficiency through Iterative Screening Using Docking and Conformal Prediction. Journal of chemical information and modeling\| PubMed ID: 28195474	2017
Toward Understanding the Cold, Hot, and Neutral Nature of Chinese Medicines Using in Silico Mode-of-Action Analysis. Journal of chemical information and modeling\| PubMed ID: 28257573	2017
Concordance analysis of microarray studies identifies representative gene expression changes in Parkinson's disease: a comparison of 33 human and animal studies. BMC neurology\| PubMed ID: 28335819	2017
Identification of Novel Class of Triazolo-Thiadiazoles as Potent Inhibitors of Human Heparanase and their Anticancer Activity. BMC cancer\| PubMed ID: 28359266	2017
Prediction of Antibiotic Interactions Using Descriptors Derived from Molecular Structure. Journal of medicinal chemistry\| PubMed ID: 28383902	2017
Polypharmacological in Silico Bioactivity Profiling and Experimental Validation Uncovers Sedative-Hypnotic Effects of Approved and Experimental Drugs in Rat. ACS chemical biology\| PubMed ID: 28414209	2017
Neighbours of cancer-related proteins have key influence on pathogenesis and could increase the drug target space for anticancer therapies. NPJ systems biology and applications\| PubMed ID: 28603644	2017
Towards understanding polyol additive effects on the pH shift-induced aggregation of a monoclonal antibody using high throughput screening and quantitative structure-activity modeling. International journal of pharmaceutics\| PubMed ID: 28754511	2017
Fragment-Based Drug Discovery of Phosphodiesterase Inhibitors. Journal of medicinal chemistry\| PubMed ID: 28800229	2018
Fast, Quantitative and Variant Enabled Mapping of Peptides to Genomes. Cell systems\| PubMed ID: 28837811	2017
Orthologue chemical space and its influence on target prediction. Bioinformatics (Oxford, England)\| PubMed ID: 28961699	2018
Innovation in Small-Molecule-Druggable Chemical Space: Where are the Initial Modulators of New Targets Published? Journal of chemical information and modeling\| PubMed ID: 29068231	2017
Identification of Novel Aurora Kinase A (AURKA) Inhibitors via Hierarchical Ligand-Based Virtual Screening. Journal of chemical information and modeling\| PubMed ID: 29202231	2018
Predicting Genes Involved in Human Cancer Using Network Contextual Information. Journal of integrative bioinformatics\| PubMed ID: 29220888	2012
DeepSynergy: predicting anti-cancer drug synergy with Deep Learning. Bioinformatics (Oxford, England)\| PubMed ID: 29253077	2018
11th German Conference on Chemoinformatics (GCC 2015) : Fulda, Germany. 8-10 November 2015. Journal of cheminformatics\| PubMed ID: 29270804	2016
Computer-aided design of multi-target ligands at AR, AR and PDE10A, key proteins in neurodegenerative diseases. Journal of cheminformatics\| PubMed ID: 29290010	2017
Common structural and pharmacophoric features of mPGES-1 and LTC4S. Future medicinal chemistry\| PubMed ID: 29355395	2018
Maximizing gain in high-throughput screening using conformal prediction. Journal of cheminformatics\| PubMed ID: 29468427	2018
eMolTox: prediction of molecular toxicity with confidence. Bioinformatics (Oxford, England)\| PubMed ID: 29522123	2018
Special Issue: Cheminformatics in Drug Discovery. ChemMedChem\| PubMed ID: 29575670	2018
A systematic and prospectively validated approach for identifying synergistic drug combinations against malaria. Malaria journal\| PubMed ID: 29642892	2018
Conformal Regression for Quantitative Structure-Activity Relationship Modeling-Quantifying Prediction Uncertainty. Journal of chemical information and modeling\| PubMed ID: 29701973	2018