| Year |
Citation |
Score |
| 2024 |
Seal S, Spjuth O, Hosseini-Gerami L, García-Ortegón M, Singh S, Bender A, Carpenter AE. Insights into Drug Cardiotoxicity from Biological and Chemical Data: The First Public Classifiers for FDA Drug-Induced Cardiotoxicity Rank. Journal of Chemical Information and Modeling. PMID 38300851 DOI: 10.1021/acs.jcim.3c01834 |
0.307 |
|
| 2023 |
Seal S, Spjuth O, Hosseini-Gerami L, García-Ortegón M, Singh S, Bender A, Carpenter AE. Insights into Drug Cardiotoxicity from Biological and Chemical Data: The First Public Classifiers for FDA DICTrank. Biorxiv : the Preprint Server For Biology. PMID 37905146 DOI: 10.1101/2023.10.15.562398 |
0.336 |
|
| 2023 |
Liu A, Seal S, Yang H, Bender A. Using chemical and biological data to predict drug toxicity. Slas Discovery : Advancing Life Sciences R & D. PMID 36639032 DOI: 10.1016/j.slasd.2022.12.003 |
0.32 |
|
| 2022 |
García-Ortegón M, Simm GNC, Tripp AJ, Hernández-Lobato JM, Bender A, Bacallado S. DOCKSTRING: Easy Molecular Docking Yields Better Benchmarks for Ligand Design. Journal of Chemical Information and Modeling. 62: 3486-3502. PMID 35849793 DOI: 10.1021/acs.jcim.1c01334 |
0.317 |
|
| 2022 |
Trapotsi MA, Mouchet E, Williams G, Monteverde T, Juhani K, Turkki R, Miljković F, Martinsson A, Mervin L, Pryde KR, Müllers E, Barrett I, Engkvist O, Bender A, Moreau K. Cell Morphological Profiling Enables High-Throughput Screening for PROteolysis TArgeting Chimera (PROTAC) Phenotypic Signature. Acs Chemical Biology. 17: 1733-1744. PMID 35793809 DOI: 10.1021/acschembio.2c00076 |
0.306 |
|
| 2021 |
Thomas M, Smith RT, O'Boyle NM, de Graaf C, Bender A. Comparison of structure- and ligand-based scoring functions for deep generative models: a GPCR case study. Journal of Cheminformatics. 13: 39. PMID 33985583 DOI: 10.1186/s13321-021-00516-0 |
0.351 |
|
| 2021 |
Trapotsi MA, Mervin LH, Afzal AM, Sturm N, Engkvist O, Barrett IP, Bender A. Comparison of Chemical Structure and Cell Morphology Information for Multitask Bioactivity Predictions. Journal of Chemical Information and Modeling. PMID 33661004 DOI: 10.1021/acs.jcim.0c00864 |
0.322 |
|
| 2021 |
Kalash L, Winfield I, Safitri D, Bermudez M, Carvalho S, Glen R, Ladds G, Bender A. Structure-based identification of dual ligands at the AR and PDE10A with anti-proliferative effects in lung cancer cell-lines. Journal of Cheminformatics. 13: 17. PMID 33658076 DOI: 10.1186/s13321-021-00492-5 |
0.568 |
|
| 2020 |
Cortés-Ciriano I, Škuta C, Bender A, Svozil D. QSAR-derived affinity fingerprints (part 2): modeling performance for potency prediction. Journal of Cheminformatics. 12: 41. PMID 33431016 DOI: 10.1186/S13321-020-00444-5 |
0.475 |
|
| 2020 |
Pruteanu LL, Kopanitsa L, Módos D, Kletnieks E, Samarova E, Bender A, Gomez LD, Bailey DS. Transcriptomics predicts compound synergy in drug and natural product treated glioblastoma cells. Plos One. 15: e0239551. PMID 32946518 DOI: 10.1371/Journal.Pone.0239551 |
0.343 |
|
| 2020 |
Mervin L, Afzal AM, Engkvist O, Bender A. A Comparison Of Scaling Methods To Obtain Calibrated Probabilities Of Activity For Protein-Ligand Predictions. Journal of Chemical Information and Modeling. PMID 32865408 DOI: 10.1021/Acs.Jcim.0C00476 |
0.427 |
|
| 2020 |
Škuta C, Cortés-Ciriano I, Dehaen W, Kříž P, van Westen GJP, Tetko IV, Bender A, Svozil D. QSAR-derived affinity fingerprints (part 1): fingerprint construction and modeling performance for similarity searching, bioactivity classification and scaffold hopping Journal of Cheminformatics. 12. DOI: 10.1186/S13321-020-00443-6 |
0.401 |
|
| 2019 |
Vlot AHC, Aniceto N, Menden MP, Ulrich-Merzenich G, Bender A. Applying drug synergy metrics to oncology combination screening data: agreements, disagreements and pitfalls. Drug Discovery Today. PMID 31518641 DOI: 10.1016/J.Drudis.2019.09.002 |
0.364 |
|
| 2019 |
Drakakis G, Cortés-Ciriano I, Alexander-Dann B, Bender A. Elucidating Compound Mechanism of Action and Predicting Cytotoxicity Using Machine Learning Approaches, Taking Prediction Confidence into Account. Current Protocols in Chemical Biology. 11: e73. PMID 31483099 DOI: 10.1002/Cpch.73 |
0.399 |
|
| 2019 |
Mahmoud SY, Svensson F, Zoufir A, Modos D, Afzal AM, Bender A. Understanding conditional associations between ToxCast in vitro readouts and the hepatotoxicity of compounds using rule-based methods. Chemical Research in Toxicology. PMID 31442032 DOI: 10.1021/Acs.Chemrestox.8B00382 |
0.352 |
|
| 2019 |
Rangappa K, Keerthy HK, Mohan S, Basappa B, Rangappa S, Bharathkumar H, Svensson F, Bender A, Mohan CD, Bhatnagar R. Triazole-Pyridine Dicarbonitrile Targets Phosphodiesterase 4 to Induce Anticancer Activity in Lung Carcinoma Cells. Chemistry & Biodiversity. PMID 31287204 DOI: 10.1002/Cbdv.201900234 |
0.361 |
|
| 2019 |
Cortés-Ciriano I, Bender A. Reliable Prediction Errors for Deep Neural Networks Using Test-Time Dropout. Journal of Chemical Information and Modeling. PMID 31241929 DOI: 10.1021/Acs.Jcim.9B00297 |
0.35 |
|
| 2019 |
Cortés-Ciriano I, Bender A. KekuleScope: prediction of cancer cell line sensitivity and compound potency using convolutional neural networks trained on compound images. Journal of Cheminformatics. 11: 41. PMID 31218493 DOI: 10.1186/S13321-019-0364-5 |
0.432 |
|
| 2019 |
Allen CHG, Mervin LH, Mahmoud SY, Bender A. Leveraging heterogeneous data from GHS toxicity annotations, molecular and protein target descriptors and Tox21 assay readouts to predict and rationalise acute toxicity. Journal of Cheminformatics. 11: 36. PMID 31152262 DOI: 10.1186/S13321-019-0356-5 |
0.453 |
|
| 2019 |
Sokolov A, Ashenden S, Sahin N, Lewis R, Erdem N, Ozaltan E, Bender A, Roth FP, Cokol M. Characterizing ABC-Transporter Substrate-Likeness Using a Clean-Slate Genetic Background. Frontiers in Pharmacology. 10: 448. PMID 31105571 DOI: 10.3389/Fphar.2019.00448 |
0.308 |
|
| 2019 |
Mazzolari A, Afzal AM, Pedretti A, Testa B, Vistoli G, Bender A. Prediction of UGT-mediated Metabolism Using the Manually Curated MetaQSAR Database. Acs Medicinal Chemistry Letters. 10: 633-638. PMID 30996809 DOI: 10.1021/Acsmedchemlett.8B00603 |
0.332 |
|
| 2019 |
Basappa B, mOHAN S, Rangappa S, Anilkumar NC, Fuchs JE, Bender A, Ks R, Bhatnagar R. Sulfated ceria catalyzed synthesis of imidazopyridines and their implementation as DNA minor groove binders. Chemistry & Biodiversity. PMID 30702795 DOI: 10.1002/Cbdv.201800435 |
0.351 |
|
| 2018 |
Noori HR, Mervin LH, Bokharaie V, Durmus Ö, Egenrieder L, Fritze S, Gruhlke B, Reinhardt G, Schabel HH, Staudenmaier S, Logothetis NK, Bender A, Spanagel R. Systemic neurotransmitter responses to clinically approved and experimental neuropsychiatric drugs. Nature Communications. 9: 4699. PMID 30410047 DOI: 10.1038/S41467-018-07239-1 |
0.323 |
|
| 2018 |
Chang L, Xiao M, Yang L, Wang S, Wang SQ, Bender A, Hu A, Chen ZS, Yu B, Liu HM. Discovery of a non-toxic [1,2,4]triazolo[1,5-a]pyrimidin-7-one (WS-10) that modulates ABCB1-mediated multidrug resistance (MDR). Bioorganic & Medicinal Chemistry. PMID 30401501 DOI: 10.1016/J.Bmc.2018.10.027 |
0.32 |
|
| 2018 |
Svensson F, Zoufir A, Mahmoud S, Afzal AM, Smit I, Giblin KA, Clements PJ, Mettetal JT, Pointon A, Harvey JS, Greene N, Williams RV, Bender A. Information-Derived Mechanistic Hypotheses for Structural Cardiotoxicity. Chemical Research in Toxicology. PMID 30350600 DOI: 10.1021/Acs.Chemrestox.8B00159 |
0.326 |
|
| 2018 |
Cortés-Ciriano I, Bender A. Deep Confidence: A Computationally Efficient Framework for Calculating Reliable Prediction Errors for Deep Neural Networks. Journal of Chemical Information and Modeling. PMID 30336009 DOI: 10.1021/Acs.Jcim.8B00542 |
0.357 |
|
| 2018 |
Mason DJ, Eastman RT, Lewis RPI, Stott IP, Guha R, Bender A. Using Machine Learning to Predict Synergistic Antimalarial Compound Combinations With Novel Structures. Frontiers in Pharmacology. 9: 1096. PMID 30333748 DOI: 10.3389/Fphar.2018.01096 |
0.469 |
|
| 2018 |
Pandey V, Wang B, Mohan CD, Raquib AR, Rangappa S, Srinivasa V, Fuchs JE, Girish KS, Zhu T, Bender A, Ma L, Yin Z, Basappa, Rangappa KS, Lobie PE. Discovery of a small-molecule inhibitor of specific serine residue BAD phosphorylation. Proceedings of the National Academy of Sciences of the United States of America. PMID 30309962 DOI: 10.1073/Pnas.1804897115 |
0.323 |
|
| 2018 |
Kalash L, Cresser-Brown J, Habchi J, Morgan C, Miller DJ, Glen RC, Allemann RK, Bender A. Structure-based design of allosteric calpain-1 inhibitors populating a novel bioactivity space. European Journal of Medicinal Chemistry. 157: 1264-1275. PMID 30195237 DOI: 10.1016/J.Ejmech.2018.08.049 |
0.599 |
|
| 2018 |
Oerton E, Roberts I, Lewis PSH, Guilliams T, Bender A. Understanding and predicting disease relationships through similarity fusion. Bioinformatics (Oxford, England). PMID 30169824 DOI: 10.1093/Bioinformatics/Bty754 |
0.32 |
|
| 2018 |
Cortés Ciriano I, Firth N, Bender A, Watson O. Discovering Highly Potent Molecules from an Initial Set of Inactives Using Iterative Screening. Journal of Chemical Information and Modeling. PMID 30130102 DOI: 10.1021/Acs.Jcim.8B00376 |
0.445 |
|
| 2018 |
Giblin K, Hughes S, Boyd H, Hansson P, Bender A. Prospectively Validated Proteochemometric Models for the Prediction of Small Molecule Binding to Bromodomain Proteins. Journal of Chemical Information and Modeling. PMID 30125501 DOI: 10.1021/Acs.Jcim.8B00400 |
0.489 |
|
| 2018 |
Mateu N, Kidd SL, Kalash L, Sore HF, Madin A, Bender A, Spring DR. Synthesis of structurally diverse N-substituted quaternary carbon containing small molecules from α,α-disubstituted propargyl amino esters. Chemistry (Weinheim An Der Bergstrasse, Germany). PMID 30011115 DOI: 10.1002/Chem.201803143 |
0.345 |
|
| 2018 |
Mervin LH, Afzal AM, Brive L, Engkvist O, Bender A. Extending Protein Target Prediction Models to Include Functional Effects. Frontiers in Pharmacology. 9: 613. PMID 29942259 DOI: 10.3389/Fphar.2018.00613 |
0.464 |
|
| 2018 |
Svensson F, Aniceto N, Norinder U, Cortes-Ciriano I, Spjuth O, Carlsson L, Bender A. Conformal Regression for QSAR Modelling - Quantifying Prediction Uncertainty. Journal of Chemical Information and Modeling. PMID 29701973 DOI: 10.1021/Acs.Jcim.8B00054 |
0.358 |
|
| 2018 |
Ji C, Svensson F, Zoufir A, Bender A. eMolTox: prediction of molecular toxicity with confidence. Bioinformatics (Oxford, England). PMID 29522123 DOI: 10.1093/Bioinformatics/Bty135 |
0.358 |
|
| 2018 |
Svensson F, Afzal AM, Norinder U, Bender A. Maximizing gain in high-throughput screening using conformal prediction. Journal of Cheminformatics. 10: 7. PMID 29468427 DOI: 10.1186/S13321-018-0260-4 |
0.397 |
|
| 2018 |
Devi NS, Paragi-Vedanthi P, Bender A, Doble M. Common structural and pharmacophoric features of mPGES-1 and LTC4S. Future Medicinal Chemistry. PMID 29355395 DOI: 10.4155/Fmc-2017-0123 |
0.369 |
|
| 2017 |
Subramanian V, Ain QU, Henno H, Pietilä LO, Fuchs JE, Prusis P, Bender A, Wohlfahrt G. 3D proteochemometrics: using three-dimensional information of proteins and ligands to address aspects of the selectivity of serine proteases. Medchemcomm. 8: 1037-1045. PMID 30108817 DOI: 10.1039/C6Md00701E |
0.386 |
|
| 2017 |
Svensson F, Norinder U, Bender A. Modelling compound cytotoxicity using conformal prediction and PubChem HTS data. Toxicology Research. 6: 73-80. PMID 30090478 DOI: 10.1039/C6Tx00252H |
0.445 |
|
| 2017 |
Kalash L, Val C, Azuaje J, Loza MI, Svensson F, Zoufir A, Mervin L, Ladds G, Brea J, Glen R, Sotelo E, Bender A. Computer-aided design of multi-target ligands at A1R, A2AR and PDE10A, key proteins in neurodegenerative diseases. Journal of Cheminformatics. 9: 67. PMID 29290010 DOI: 10.1186/S13321-017-0249-4 |
0.637 |
|
| 2017 |
Preuer K, Lewis RPI, Hochreiter S, Bender A, Bulusu KC, Klambauer G. DeepSynergy: Predicting anti-cancer drug synergy with Deep Learning. Bioinformatics (Oxford, England). PMID 29253077 DOI: 10.1093/Bioinformatics/Btx806 |
0.77 |
|
| 2017 |
Kong Y, Bender A, Yan A. Identification of Novel Aurora Kinase A (AURKA) Inhibitors via Hierarchical Ligand-Based Virtual Screening. Journal of Chemical Information and Modeling. PMID 29202231 DOI: 10.1021/Acs.Jcim.7B00300 |
0.395 |
|
| 2017 |
Ashenden SK, Kogej T, Engkvist O, Bender A. Innovation in Small-Molecule-Druggable Chemical Space: Where are the Initial Modulators of New Targets Published? Journal of Chemical Information and Modeling. PMID 29068231 DOI: 10.1021/Acs.Jcim.7B00295 |
0.404 |
|
| 2017 |
Mervin LH, Bulusu KC, Kalash L, Afzal A, Svensson F, Firth MA, Barrett I, Engkvist O, Bender A. Orthologue chemical space and its influence on target prediction. Bioinformatics (Oxford, England). PMID 28961699 DOI: 10.1093/Bioinformatics/Btx525 |
0.785 |
|
| 2017 |
Svensson F, Bender A, Bailey D. Fragment-Based Drug Discovery of Phosphodiesterase Inhibitors. Journal of Medicinal Chemistry. PMID 28800229 DOI: 10.1021/Acs.Jmedchem.7B00404 |
0.356 |
|
| 2017 |
Oyetayo OO, Méndez-Lucio O, Bender A, Kiefer H. 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. PMID 28754511 DOI: 10.1016/J.Ijpharm.2017.07.059 |
0.341 |
|
| 2017 |
Módos D, Bulusu KC, Fazekas D, Kubisch J, Brooks J, Marczell I, Szabó PM, Vellai T, Csermely P, Lenti K, Bender A, Korcsmáros T. 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. 3: 2. PMID 28603644 DOI: 10.1038/s41540-017-0003-6 |
0.744 |
|
| 2017 |
Drakakis G, Wafford KA, Brewerton SC, Bodkin MJ, Evans DA, Bender A. Polypharmacological In Silico Bioactivity Profiling and Experimental Validation Uncovers Sedative-Hypnotic Effects of Approved and Experimental Drugs in Rat. Acs Chemical Biology. PMID 28414209 DOI: 10.1021/Acschembio.7B00209 |
0.384 |
|
| 2017 |
Mason DJ, Stott IP, Ashenden SK, Weinstein ZB, Karakoc I, Meral S, Kuru N, Bender A, Cokol M. Prediction of antibiotic interactions using descriptors derived from compound molecular structure. Journal of Medicinal Chemistry. PMID 28383902 DOI: 10.1021/Acs.Jmedchem.7B00204 |
0.382 |
|
| 2017 |
Baburajeev CP, Mohan CD, Rangappa S, Mason DJ, Fuchs JE, Bender A, Barash U, Vlodavsky I, Basappa, Rangappa KS. Identification of Novel Class of Triazolo-Thiadiazoles as Potent Inhibitors of Human Heparanase and their Anticancer Activity. Bmc Cancer. 17: 235. PMID 28359266 DOI: 10.1186/S12885-017-3214-8 |
0.337 |
|
| 2017 |
Fu X, Mervin LH, Li X, Yu H, Li J, Mohamad Zobir SZ, Zoufir A, Zhou Y, Song Y, Wang Z, Bender A. Towards understanding the cold, hot, and neutral Nature of Chinese medicines using in silico mode-of-action analysis. Journal of Chemical Information and Modeling. PMID 28257573 DOI: 10.1021/Acs.Jcim.6B00725 |
0.357 |
|
| 2017 |
Svensson F, Norinder U, Bender A. Improving Screening Efficiency through Iterative Screening Using Docking and Conformal Prediction. Journal of Chemical Information and Modeling. PMID 28195474 DOI: 10.1021/Acs.Jcim.6B00532 |
0.417 |
|
| 2017 |
Kavanagh ME, Chenge J, Zoufir A, McLean KJ, Coyne AG, Bender A, Munro AW, Abell C. A fragment profiling approach to inhibitors of the orphan M. tuberculosis P450 CYP144A1. Biochemistry. PMID 28169518 DOI: 10.1021/Acs.Biochem.6B00954 |
0.333 |
|
| 2017 |
Weinstein ZB, Bender A, Cokol M. Prediction of synergistic drug combinations Current Opinion in Systems Biology. 4: 24-28. DOI: 10.1016/J.Coisb.2017.05.005 |
0.385 |
|
| 2017 |
Wong KK, Mervin LH, Mazzolari A, Bender A, Yaacob NS. Towards the mode of action of Strobilanthes crispus through integrated computational and experimental analyses Journal of Plant Biochemistry and Biotechnology. 26: 451-466. DOI: 10.1007/S13562-017-0407-9 |
0.416 |
|
| 2016 |
Allen CHG, Koutsoukas A, Cortés-Ciriano I, Murrell DS, Malliavin TE, Glen RC, Bender A. Improving the prediction of organism-level toxicity through integration of chemical, protein target and cytotoxicity qHTS data. Toxicology Research. 5: 883-894. PMID 30090397 DOI: 10.1039/C5Tx00406C |
0.664 |
|
| 2016 |
Sebastian A, Pandey V, Mohan CD, Chia YT, Rangappa S, Mathai J, Baburajeev CP, Paricharak S, Mervin LH, Bulusu KC, Fuchs JE, Bender A, Yamada S, Basappa, Lobie PE, et al. Novel Adamantanyl-Based Thiadiazolyl Pyrazoles Targeting EGFR in Triple-Negative Breast Cancer. Acs Omega. 1: 1412-1424. PMID 30023509 DOI: 10.1021/acsomega.6b00251 |
0.745 |
|
| 2016 |
Fechner U, de Graaf C, Torda AE, Güssregen S, Evers A, Matter H, Hessler G, Richmond NJ, Schmidtke P, Segler MHS, Waller MP, Pleik S, Shea JE, Levine Z, Mullen R, ... ... Bender A, ... ... Bender A, ... ... Bender A, et al. 11th German Conference on Chemoinformatics (GCC 2015) : Fulda, Germany. 8-10 November 2015. Journal of Cheminformatics. 8: 18. PMID 29270804 DOI: 10.1186/S13321-016-0119-5 |
0.737 |
|
| 2016 |
Sharma N, Pulito C, Klambauer G, Mattoli L, Strano S, Blandino G, Lucci J, Bender A. Anti-mesothelioma mechanism of action studies of a complex Cynara scolymus fraction using in silico target prediction and gene expression profiling. Planta Medica. 81: S1-S381. PMID 27975443 DOI: 10.1055/S-0036-1596242 |
0.311 |
|
| 2016 |
Oyetayo OO, Méndez-Lucio O, Bender A, Kiefer H. 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. 97: 151-157. PMID 27866015 DOI: 10.1016/J.Ejps.2016.11.016 |
0.363 |
|
| 2016 |
Chiddarwar RK, Rohrer SG, Wolf A, Tresch S, Wollenhaupt S, Bender A. In silico target prediction for elucidating the mode of action of herbicides including prospective validation. Journal of Molecular Graphics & Modelling. 71: 70-79. PMID 27846423 DOI: 10.1016/J.Jmgm.2016.10.021 |
0.464 |
|
| 2016 |
Paricharak S, Méndez-Lucio O, Chavan Ravindranath A, Bender A, IJzerman AP, van Westen GJ. Data-driven approaches used for compound library design, hit triage and bioactivity modeling in high-throughput screening. Briefings in Bioinformatics. PMID 27789427 DOI: 10.1093/Bib/Bbw105 |
0.784 |
|
| 2016 |
Cortes-Ciriano I, Mervin LH, Bender A. Current Trends in Drug Sensitivity Prediction. Current Pharmaceutical Design. 22: 6918-6927. PMID 27784247 DOI: 10.2174/1381612822666161026154430 |
0.339 |
|
| 2016 |
Ain QU, Owen RM, Omoto K, Torella R, Bulusu KC, Pryde DC, Glen RC, Fuchs JE, Bender A. ANALYSIS OF DIFFERENTIAL EFFICACY AND AFFINITY OF GABAA (α1/α2) SELECTIVE MODULATORS. Molecular Pharmaceutics. PMID 27704838 DOI: 10.1021/Acs.Molpharmaceut.6B00813 |
0.77 |
|
| 2016 |
Peragovics Á, Simon Z, Málnási-Csizmadia A, Bender A. Modeling Polypharmacological Profiles by Affinity Fingerprinting. Current Pharmaceutical Design. PMID 27587199 DOI: 10.2174/1381612822666160831104718 |
0.449 |
|
| 2016 |
Aniceto N, Freitas AA, Bender A, Ghafourian T. Simultaneous Prediction of four ATP-binding Cassette Transporters' Substrates Using Multi-label QSAR. Molecular Informatics. 35: 514-528. PMID 27582431 DOI: 10.1002/Minf.201600036 |
0.361 |
|
| 2016 |
Mervin LH, Cao Q, Barrett IP, Firth MA, Murray D, McWilliams L, Haddrick M, Wigglesworth M, Engkvist O, Bender A. Understanding Cytotoxicity and Cytostaticity in a High-Throughput Screening Collection. Acs Chemical Biology. PMID 27571164 DOI: 10.1021/Acschembio.6B00538 |
0.481 |
|
| 2016 |
KalantarMotamedi Y, Peymani M, Baharvand H, Nasr-Esfahani MH, Bender A. Systematic selection of small molecules to promote differentiation of embryonic stem cells and experimental validation for generating cardiomyocytes. Cell Death Discovery. 2: 16007. PMID 27551501 DOI: 10.1038/Cddiscovery.2016.7 |
0.319 |
|
| 2016 |
Paricharak S, IJzerman AP, Jenkins JL, Bender A, Nigsch F. Data-driven Derivation of an "Informer Compound Set" for Improved Selection of Active Compounds in High-Throughput Screening. Journal of Chemical Information and Modeling. PMID 27487177 DOI: 10.1021/Acs.Jcim.6B00244 |
0.575 |
|
| 2016 |
Subramanian G, Babu Rajeev CP, Mohan CD, Sinha A, Chu TT, Anusha S, Ximei H, Fuchs JE, Bender A, Rangappa KS, Chandramohanadas R, Basappa. Synthesis and in vitro evaluation of hydrazinyl phthalazines against malaria parasite, Plasmodium falciparum. Bioorganic & Medicinal Chemistry Letters. PMID 27261180 DOI: 10.1016/J.Bmcl.2016.05.049 |
0.338 |
|
| 2016 |
Mohan CD, Srinivasa V, Rangappa S, Mervin L, Mohan S, Paricharak S, Baday S, Li F, Shanmugam MK, Chinnathambi A, Zayed ME, Alharbi SA, Bender A, Sethi G, Basappa, et al. Trisubstituted-Imidazoles Induce Apoptosis in Human Breast Cancer Cells by Targeting the Oncogenic PI3K/Akt/mTOR Signaling Pathway. Plos One. 11: e0153155. PMID 27097161 DOI: 10.1371/Journal.Pone.0153155 |
0.339 |
|
| 2016 |
Mohamad Zobir SZ, Mohd Fauzi F, Liggi S, Drakakis G, Fu X, Fan TP, Bender A. Global Mapping of Traditional Chinese Medicine into Bioactivity Space and Pathways Annotation Improves Mechanistic Understanding and Discovers Relationships between Therapeutic Action (Sub)classes. Evidence-Based Complementary and Alternative Medicine : Ecam. 2016: 2106465. PMID 26989424 DOI: 10.1155/2016/2106465 |
0.399 |
|
| 2016 |
Paricharak S, IJzerman AP, Bender A, Nigsch F. Analysis of Iterative Screening with Stepwise Compound Selection Based on Novartis In-house HTS Data. Acs Chemical Biology. 11: 1255-64. PMID 26878899 DOI: 10.1021/Acschembio.6B00029 |
0.56 |
|
| 2016 |
Rahmani H, Weiss G, Méndez-Lucio O, Bender A. ARWAR: A network approach for predicting Adverse Drug Reactions. Computers in Biology and Medicine. 68: 101-8. PMID 26638149 DOI: 10.1016/J.Compbiomed.2015.11.005 |
0.326 |
|
| 2016 |
Cortés-Ciriano I, Bender A. How Consistent are Publicly Reported Cytotoxicity Data? Large-Scale Statistical Analysis of the Concordance of Public Independent Cytotoxicity Measurements. Chemmedchem. 11: 57-71. PMID 26541361 DOI: 10.1002/Cmdc.201500424 |
0.364 |
|
| 2016 |
Aniceto N, Freitas AA, Bender A, Ghafourian T. A novel applicability domain technique for mapping predictive reliability across the chemical space of a QSAR: reliability-density neighbourhood Journal of Cheminformatics. 8: 69. DOI: 10.1186/S13321-016-0182-Y |
0.37 |
|
| 2016 |
Kumar KH, Paricharak S, Mohan CD, Bharathkumar H, Nagabhushana GP, Rajashekar DK, Chandrappa GT, Bender A, Basappa, Rangappa KS. Nano-MoO3-mediated synthesis of bioactive thiazolidin-4-ones acting as anti-bacterial agents and their mode-of-action analysis using in silico target prediction, docking and similarity searching New Journal of Chemistry. 40: 2189-2199. DOI: 10.1039/C5Nj02729B |
0.401 |
|
| 2015 |
Cortés-Ciriano I, Bender A, Malliavin T. Prediction of PARP Inhibition with Proteochemometric Modelling and Conformal Prediction. Molecular Informatics. 34: 357-66. PMID 27490382 DOI: 10.1002/Minf.201400165 |
0.389 |
|
| 2015 |
Anusha S, Mohan CD, Ananda H, Baburajeev CP, Rangappa S, Mathai J, Fuchs JE, Li F, Shanmugam MK, Bender A, Sethi G, Basappa, Rangappa KS. Adamantyl-tethered-biphenylic compounds induce apoptosis in cancer cells by targeting Bcl homologs. Bioorganic & Medicinal Chemistry Letters. PMID 26725030 DOI: 10.1016/J.Bmcl.2015.12.026 |
0.368 |
|
| 2015 |
Cortes-Ciriano I, Bender A. Improved Chemical Structure-Activity Modeling Through Data Augmentation. Journal of Chemical Information and Modeling. 55: 2682-92. PMID 26619900 DOI: 10.1021/Acs.Jcim.5B00570 |
0.386 |
|
| 2015 |
Mervin LH, Afzal AM, Drakakis G, Lewis R, Engkvist O, Bender A. Target prediction utilising negative bioactivity data covering large chemical space. Journal of Cheminformatics. 7: 51. PMID 26500705 DOI: 10.1186/S13321-015-0098-Y |
0.441 |
|
| 2015 |
Anusha S, Cp B, Mohan CD, Mathai J, Rangappa S, Mohan S, Chandra, Paricharak S, Mervin L, Fuchs JE, M M, Bender A, Basappa, Rangappa KS. 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. 10: e0139798. PMID 26470029 DOI: 10.1371/Journal.Pone.0139798 |
0.339 |
|
| 2015 |
Fuchs JE, Bender A, Glen RC. Cheminformatics Research at the Unilever Centre for Molecular Science Informatics Cambridge. Molecular Informatics. 34: 626-633. PMID 26435758 DOI: 10.1002/Minf.201400166 |
0.534 |
|
| 2015 |
Baburajeev CP, Dhananjaya Mohan C, Ananda H, Rangappa S, Fuchs JE, Jagadish S, Sivaraman Siveen K, Chinnathambi A, Ali Alharbi S, Zayed ME, Zhang J, Li F, Sethi G, Girish KS, Bender A, et al. Development of Novel Triazolo-Thiadiazoles from Heterogeneous "Green" Catalysis as Protein Tyrosine Phosphatase 1B Inhibitors. Scientific Reports. 5: 14195. PMID 26388336 DOI: 10.1038/Srep14195 |
0.381 |
|
| 2015 |
Bulusu KC, Guha R, Mason DJ, Lewis RP, Muratov E, Kalantar Motamedi Y, Cokol M, Bender A. Modelling of compound combination effects and applications to efficacy and toxicity: state-of-the-art, challenges and perspectives. Drug Discovery Today. PMID 26360051 DOI: 10.1016/J.Drudis.2015.09.003 |
0.792 |
|
| 2015 |
Cortés-Ciriano I, van Westen GJ, Bouvier G, Nilges M, Overington JP, Bender A, Malliavin TE. Improved large-scale prediction of growth inhibition patterns using the NCI60 cancer cell line panel. Bioinformatics (Oxford, England). PMID 26351271 DOI: 10.1093/Bioinformatics/Btv529 |
0.786 |
|
| 2015 |
Anusha S, Sinha A, Babu Rajeev CP, Chu TT, Mathai J, Ximei H, Fuchs JE, Shivananju N, Bender A, Preiser PR, Rangappa KS, Basappa, Chandramohanadas R. Synthesis, characterization and in vitro evaluation of novel enantiomerically-pure sulphonamide antimalarials. Organic & Biomolecular Chemistry. PMID 26347024 DOI: 10.1039/C5Ob01479D |
0.365 |
|
| 2015 |
Murrell DS, Cortes-Ciriano I, van Westen GJ, Stott IP, Bender A, Malliavin TE, Glen RC. Chemically Aware Model Builder (camb): an R package for property and bioactivity modelling of small molecules. Journal of Cheminformatics. 7: 45. PMID 26322135 DOI: 10.1186/S13321-015-0086-2 |
0.792 |
|
| 2015 |
Ashwini N, Garg M, Mohan CD, Fuchs JE, Rangappa S, Anusha S, Swaroop TR, Rakesh KS, Kanojia D, Madan V, Bender A, Koeffler HP, Basappa, Rangappa KS. 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 acetylation. Bioorganic & Medicinal Chemistry. 23: 6157-65. PMID 26299825 DOI: 10.1016/J.Bmc.2015.07.069 |
0.386 |
|
| 2015 |
Lewis R, Guha R, Korcsmaros T, Bender A. Synergy Maps: exploring compound combinations using network-based visualization. Journal of Cheminformatics. 7: 36. PMID 26236402 DOI: 10.1186/S13321-015-0090-6 |
0.38 |
|
| 2015 |
De Lucia D, Lucio OM, Musio B, Bender A, Listing M, Dennhardt S, Koeberle A, Garscha U, Rizzo R, Manfredini S, Werz O, Ley SV. Design, synthesis and evaluation of semi-synthetic triazole-containing caffeic acid analogues as 5-lipoxygenase inhibitors. European Journal of Medicinal Chemistry. 101: 573-83. PMID 26197161 DOI: 10.1016/J.Ejmech.2015.07.011 |
0.404 |
|
| 2015 |
Anilkumar NC, Sundaram MS, Mohan CD, Rangappa S, Bulusu KC, Fuchs JE, Girish KS, Bender A, Basappa, Rangappa KS. A One Pot Synthesis of Novel Bioactive Tri-Substitute-Condensed-Imidazopyridines that Targets Snake Venom Phospholipase A2. Plos One. 10: e0131896. PMID 26196520 DOI: 10.1371/Journal.Pone.0131896 |
0.781 |
|
| 2015 |
Bharathkumar H, Mohan CD, Rangappa S, Kang T, Keerthy HK, Fuchs JE, Kwon NH, Bender A, Kim S, Basappa, Rangappa KS. Screening of quinoline, 1,3-benzoxazine, and 1,3-oxazine-based small molecules against isolated methionyl-tRNA synthetase and A549 and HCT116 cancer cells including an in silico binding mode analysis. Organic & Biomolecular Chemistry. 13: 9381-7. PMID 26159576 DOI: 10.1039/C5Ob00791G |
0.392 |
|
| 2015 |
Mak L, Marcus D, Howlett A, Yarova G, Duchateau G, Klaffke W, Bender A, Glen RC. Metrabase: a cheminformatics and bioinformatics database for small molecule transporter data analysis and (Q)SAR modeling. Journal of Cheminformatics. 7: 31. PMID 26106450 DOI: 10.1186/S13321-015-0083-5 |
0.581 |
|
| 2015 |
Afzal AM, Mussa HY, Turner RE, Bender A, Glen RC. A multi-label approach to target prediction taking ligand promiscuity into account. Journal of Cheminformatics. 7: 24. PMID 26064191 DOI: 10.1186/S13321-015-0071-9 |
0.643 |
|
| 2015 |
Srinivas V, Mohan CD, Baburajeev CP, Rangappa S, Jagadish S, Fuchs JE, Sukhorukov AY, Chandra, Mason DJ, Sharath Kumar KS, Madegowda M, Bender A, Basappa, Rangappa KS. Synthesis and characterization of novel oxazines and demonstration that they specifically target cyclooxygenase 2. Bioorganic & Medicinal Chemistry Letters. 25: 2931-6. PMID 26048794 DOI: 10.1016/J.Bmcl.2015.05.047 |
0.341 |
|
| 2015 |
Paricharak S, Cortés-Ciriano I, IJzerman AP, Malliavin TE, Bender A. 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. 7: 15. PMID 25926892 DOI: 10.1186/S13321-015-0063-9 |
0.621 |
|
| 2015 |
Bharathkumar H, Mohan CD, Ananda H, Fuchs JE, Li F, Rangappa S, Surender M, Bulusu KC, Girish KS, Sethi G, Bender A, Basappa, Rangappa KS. Microwave-assisted synthesis, characterization and cytotoxic studies of novel estrogen receptor α ligands towards human breast cancer cells. Bioorganic & Medicinal Chemistry Letters. 25: 1804-7. PMID 25797502 DOI: 10.1016/J.Bmcl.2015.01.030 |
0.759 |
|
| 2015 |
Drakakis G, Koutsoukas A, Brewerton SC, Bodkin MJ, Evans DA, Bender A. Comparing global and local likelihood score thresholds in multiclass laplacian-modified naive bayes protein target prediction. Combinatorial Chemistry & High Throughput Screening. 18: 323-30. PMID 25747441 DOI: 10.2174/1386207318666150305145012 |
0.393 |
|
| 2015 |
Cortes-Ciriano I, Murrell DS, van Westen GJ, Bender A, Malliavin TE. Prediction of the potency of mammalian cyclooxygenase inhibitors with ensemble proteochemometric modeling. Journal of Cheminformatics. 7: 1. PMID 25705261 DOI: 10.1186/S13321-014-0049-Z |
0.742 |
|
| 2015 |
Méndez-Lucio O, Kooistra AJ, de Graaf C, Bender A, Medina-Franco JL. Analyzing multitarget activity landscapes using protein-ligand interaction fingerprints: interaction cliffs. Journal of Chemical Information and Modeling. 55: 251-62. PMID 25615841 DOI: 10.1021/Ci500721X |
0.363 |
|
| 2015 |
Verbist B, Klambauer G, Vervoort L, Talloen W, Shkedy Z, Thas O, Bender A, Göhlmann HWH, Hochreiter S. Using transcriptomics to guide lead optimization in drug discovery projects: Lessons learned from the QSTAR project Drug Discovery Today. 20: 505-513. PMID 25582842 DOI: 10.1016/J.Drudis.2014.12.014 |
0.329 |
|
| 2015 |
Ravindranath AC, Perualila-Tan N, Kasim A, Drakakis G, Liggi S, Brewerton SC, Mason D, Bodkin MJ, Evans DA, Bhagwat A, Talloen W, Göhlmann HW, Shkedy Z, Bender A. Connecting gene expression data from connectivity map and in silico target predictions for small molecule mechanism-of-action analysis. Molecular Biosystems. 11: 86-96. PMID 25254964 DOI: 10.1039/C4Mb00328D |
0.356 |
|
| 2015 |
Cortes-Ciriano I, van Westen GJ, Murrell DS, Lenselink EB, Bender A, Malliavin TE. Applications of proteochemometrics - from species extrapolation to cell line sensitivity modelling Bmc Bioinformatics. 16. DOI: 10.1186/1471-2105-16-S3-A4 |
0.448 |
|
| 2015 |
Keerthy HK, Vivek HK, Bharathkumar H, Rangappa S, Bulusu KC, Mervin LH, Fuchs JE, Priya BS, Basappa, S NS, Bender A, Rangappa KS. MOLPRINT 2D-based identification and synthesis of novel chromene based small molecules that target PLA2: validation through chemo- and bioinformatics approaches Rsc Advances. 5: 89797-89808. DOI: 10.1039/C5Ra13085A |
0.449 |
|
| 2015 |
Shehata MA, Belcik Christensen H, Isberg V, Sejer Pedersen D, Bender A, Bräuner-Osborne H, Gloriam DE. Identification of the first surrogate agonists for the G protein-coupled receptor GPR132 Rsc Advances. 5: 48551-48557. DOI: 10.1039/C5Ra04804D |
0.397 |
|
| 2015 |
Cortés-Ciriano I, Ain QU, Subramanian V, Lenselink EB, Méndez-Lucio O, Ijzerman AP, Wohlfahrt G, Prusis P, Malliavin TE, Van Westen GJP, Bender A. Polypharmacology modelling using proteochemometrics (PCM): Recent methodological developments, applications to target families, and future prospects Medchemcomm. 6: 24-50. DOI: 10.1039/C4Md00216D |
0.557 |
|
| 2014 |
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. Extending in silico mechanism-of-action analysis by annotating targets with pathways: application to cellular cytotoxicity readouts. Future Medicinal Chemistry. 6: 2029-56. PMID 25531967 DOI: 10.4155/Fmc.14.137 |
0.596 |
|
| 2014 |
van Westen GJ, Bender A, Overington JP. Towards predictive resistance models for agrochemicals by combining chemical and protein similarity via proteochemometric modelling. Journal of Chemical Biology. 7: 119-23. PMID 25320644 DOI: 10.1007/S12154-014-0112-2 |
0.793 |
|
| 2014 |
Mohan CD, Bharathkumar H, Bulusu KC, Pandey V, Rangappa S, Fuchs JE, Shanmugam MK, Dai X, Li F, Deivasigamani A, Hui KM, Kumar AP, Lobie PE, Bender A, Basappa, et al. 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. 289: 34296-307. PMID 25320076 DOI: 10.1074/Jbc.M114.601104 |
0.75 |
|
| 2014 |
Keerthy HK, Garg M, Mohan CD, Madan V, Kanojia D, Shobith R, Nanjundaswamy S, Mason DJ, Bender A, Basappa, Rangappa KS, Koeffler HP. Synthesis and characterization of novel 2-amino-chromene-nitriles that target Bcl-2 in acute myeloid leukemia cell lines. Plos One. 9: e107118. PMID 25268519 DOI: 10.1371/Journal.Pone.0107118 |
0.347 |
|
| 2014 |
Ain QU, Méndez-Lucio O, Ciriano IC, Malliavin T, van Westen GJ, Bender A. 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. 6: 1023-33. PMID 25255469 DOI: 10.1039/C4Ib00175C |
0.758 |
|
| 2014 |
Keerthy HK, Mohan CD, Sivaraman Siveen K, Fuchs JE, Rangappa S, Sundaram MS, Li F, Girish KS, Sethi G, Basappa, Bender A, Rangappa KS. Novel synthetic biscoumarins target tumor necrosis factor-α in hepatocellular carcinoma in vitro and in vivo. The Journal of Biological Chemistry. 289: 31879-90. PMID 25231984 DOI: 10.1074/Jbc.M114.593855 |
0.336 |
|
| 2014 |
Bharathkumar H, Sundaram MS, Jagadish S, Paricharak S, Hemshekhar M, Mason D, Kemparaju K, Girish KS, Basappa, Bender A, Rangappa KS. Novel benzoxazine-based aglycones block glucose uptake in vivo by inhibiting glycosidases. Plos One. 9: e102759. PMID 25047583 DOI: 10.1371/Journal.Pone.0102759 |
0.348 |
|
| 2014 |
Cortes-Ciriano I, van Westen GJ, Lenselink EB, Murrell DS, Bender A, Malliavin T. Proteochemometric modeling in a Bayesian framework. Journal of Cheminformatics. 6: 35. PMID 25045403 DOI: 10.1186/1758-2946-6-35 |
0.746 |
|
| 2014 |
Hudson SA, Mashalidis EH, Bender A, McLean KJ, Munro AW, Abell C. Biofragments: an approach towards predicting protein function using biologically related fragments and its application to Mycobacterium tuberculosis CYP126. Chembiochem : a European Journal of Chemical Biology. 15: 549-55. PMID 24677424 DOI: 10.1002/Cbic.201300697 |
0.407 |
|
| 2014 |
Koutsoukas A, Paricharak S, Galloway WR, Spring DR, Ijzerman AP, Glen RC, Marcus D, Bender A. How diverse are diversity assessment methods? A comparative analysis and benchmarking of molecular descriptor space. Journal of Chemical Information and Modeling. 54: 230-42. PMID 24289493 DOI: 10.1021/Ci400469U |
0.706 |
|
| 2014 |
Bharathkumar H, Paricharak S, Dinesh KR, Siveen KS, Fuchs JE, Rangappa S, Mohan CD, Mohandas N, Kumar AP, Sethi G, Bender A, Basappa, Rangappa KS. Synthesis, biological evaluation and in silico and in vitro mode-of-action analysis of novel dihydropyrimidones targeting PPAR-γ Rsc Advances. 4: 45143-45146. DOI: 10.1039/C4Ra08713E |
0.363 |
|
| 2014 |
Drakakis G, Hendry AE, Hanson K, Brewerton SC, Bodkin MJ, Evans DA, Wheeler GN, Bender A. Comparative mode-of-action analysis following manual and automated phenotype detection in Xenopus laevis Medchemcomm. 5: 386-396. DOI: 10.1039/C3Md00313B |
0.4 |
|
| 2014 |
Revanna CN, Srinivasa V, Li F, Siveen KS, Dai X, Swamy SN, Bhadregowda DG, Sethi G, Mantelingu K, Bender A, Ks R. Synthesis and biological evaluation of tetrahydropyridinepyrazoles ('PFPs') as inhibitors of STAT3 phosphorylation Medchemcomm. 5: 32-40. DOI: 10.1039/C3Md00119A |
0.373 |
|
| 2014 |
Bender A. Toxicity prediction using heterogeneous chemical and biological data sources Toxicology Letters. 229. DOI: 10.1016/J.Toxlet.2014.06.040 |
0.333 |
|
| 2014 |
Fauzi FM, Koutsoukas A, Lowe R, Joshi K, Fan T, Bender A. Chemoghemogenomics approaches in rationalizing compound action of traditional Chinese and Ayurvedic medicines European Journal of Integrative Medicine. 6: 131-132. DOI: 10.1016/J.Eujim.2013.12.015 |
0.343 |
|
| 2013 |
Liggi S, Drakakis G, Hendry AE, Hanson KM, Brewerton SC, Wheeler GN, Bodkin MJ, Evans DA, Bender A. Extensions to In Silico Bioactivity Predictions Using Pathway Annotations and Differential Pharmacology Analysis: Application to Xenopus laevis Phenotypic Readouts. Molecular Informatics. 32: 1009-24. PMID 27481146 DOI: 10.1002/Minf.201300102 |
0.453 |
|
| 2013 |
Paricharak S, Klenka T, Augustin M, Patel UA, Bender A. 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 on Kinases. Journal of Cheminformatics. 5: 49. PMID 24330772 DOI: 10.1186/1758-2946-5-49 |
0.368 |
|
| 2013 |
Watts CA, Richards FM, Bender A, Bond PJ, Korb O, Kern O, Riddick M, Owen P, Myers RM, Raff J, Gergely F, Jodrell DI, Ley SV. Design, synthesis, and biological evaluation of an allosteric inhibitor of HSET that targets cancer cells with supernumerary centrosomes. Chemistry & Biology. 20: 1399-410. PMID 24210220 DOI: 10.1016/J.Chembiol.2013.09.012 |
0.363 |
|
| 2013 |
Végner L, Peragovics Á, Tombor L, Jelinek B, Czobor P, Bender A, Simon Z, Málnási-Csizmadia A. Experimental confirmation of new drug-target interactions predicted by Drug Profile Matching. Journal of Medicinal Chemistry. 56: 8377-88. PMID 24088053 DOI: 10.1021/Jm400813Y |
0.404 |
|
| 2013 |
van Westen GJ, Swier RF, Cortes-Ciriano I, Wegner JK, Overington JP, Ijzerman AP, van Vlijmen HW, Bender A. Benchmarking of protein descriptor sets in proteochemometric modeling (part 2): modeling performance of 13 amino acid descriptor sets. Journal of Cheminformatics. 5: 42. PMID 24059743 DOI: 10.1186/1758-2946-5-42 |
0.788 |
|
| 2013 |
van Westen GJ, Swier RF, Wegner JK, Ijzerman AP, van Vlijmen HW, Bender A. Benchmarking of protein descriptor sets in proteochemometric modeling (part 1): comparative study of 13 amino acid descriptor sets. Journal of Cheminformatics. 5: 41. PMID 24059694 DOI: 10.1186/1758-2946-5-41 |
0.774 |
|
| 2013 |
Fauzi FM, Koutsoukas A, Lowe R, Joshi K, Fan TP, Glen RC, Bender A. Linking Ayurveda and Western medicine by integrative analysis. Journal of Ayurveda and Integrative Medicine. 4: 117-9. PMID 23930045 DOI: 10.4103/0975-9476.113882 |
0.651 |
|
| 2013 |
Koutsoukas A, Lowe R, Kalantarmotamedi Y, Mussa HY, Klaffke W, Mitchell JB, Glen RC, Bender A. 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. 53: 1957-66. PMID 23829430 DOI: 10.1021/Ci300435J |
0.659 |
|
| 2013 |
Van Berlo RJP, Winterbach W, De Groot MJL, Bender A, Verheijen PJT, Reinders MJT, De Ridder D. Efficient calculation of compound similarity based on maximum common subgraphs and its application to prediction of gene transcript levels International Journal of Bioinformatics Research and Applications. 9: 407-432. PMID 23797997 DOI: 10.1504/Ijbra.2013.054688 |
0.406 |
|
| 2013 |
Nguyen HP, Koutsoukas A, Mohd Fauzi F, Drakakis G, Maciejewski M, Glen RC, Bender A. Diversity selection of compounds based on 'protein affinity fingerprints' improves sampling of bioactive chemical space. Chemical Biology & Drug Design. 82: 252-66. PMID 23647865 DOI: 10.1111/Cbdd.12155 |
0.657 |
|
| 2013 |
van Westen GJ, Hendriks A, Wegner JK, Ijzerman AP, van Vlijmen HW, Bender A. Significantly improved HIV inhibitor efficacy prediction employing proteochemometric models generated from antivirogram data. Plos Computational Biology. 9: e1002899. PMID 23436985 DOI: 10.1371/Journal.Pcbi.1002899 |
0.796 |
|
| 2013 |
Mohd Fauzi F, Koutsoukas A, Lowe R, Joshi K, Fan TP, Glen RC, Bender A. Chemogenomics approaches to rationalizing the mode-of-action of traditional Chinese and Ayurvedic medicines. Journal of Chemical Information and Modeling. 53: 661-73. PMID 23351136 DOI: 10.1021/Ci3005513 |
0.651 |
|
| 2013 |
Fauzi FM, Koutsoukas A, Lowe R, Joshi K, Fan T, Bender A. Chemogenomics approaches to rationalising compound action of traditional Chinese and Ayurvedic medicines Journal of Cheminformatics. 5. DOI: 10.1186/1758-2946-5-S1-P44 |
0.455 |
|
| 2013 |
Drakakis G, Koutsoukas A, Brewerton SC, Evans DD, Bender A. Using machine learning techniques for rationalising phenotypic readouts from a rat sleeping model Journal of Cheminformatics. 5: 34. DOI: 10.1186/1758-2946-5-S1-P34 |
0.382 |
|
| 2013 |
Cortes-Ciriano I, Koutsoukas A, Abian O, Bender A, Velazquez-Campoy A. Experimental validation of in silico target predictions on synergistic protein targets Journal of Cheminformatics. 5: 31. DOI: 10.1186/1758-2946-5-S1-P31 |
0.442 |
|
| 2013 |
Koutsoukas A, Torella R, Drakakis G, Bender A, Glen RC. Relating GPCRs pharmacological space based on ligands chemical similarities Journal of Cheminformatics. 5. DOI: 10.1186/1758-2946-5-S1-P26 |
0.624 |
|
| 2013 |
Paricharak S, Klenka T, Augustin M, Patel UA, Bender A. Revised classification of kinases based on bioactivity data: the importance of data density and choice of visualization Journal of Cheminformatics. 5: 24. DOI: 10.1186/1758-2946-5-S1-P24 |
0.301 |
|
| 2013 |
Chiddarwar RK, Bender A, Rohrer S. In silico target prediction: identification of on- and off-targets for crop protection agents Journal of Cheminformatics. 5: 18. DOI: 10.1186/1758-2946-5-S1-P18 |
0.423 |
|
| 2013 |
Liggi S, Koutsoukas A, Motamedi YK, Glen RC, Bender A. Annotating targets with pathways: extending approaches to mode of action analysis Journal of Cheminformatics. 5. DOI: 10.1186/1758-2946-5-S1-P15 |
0.629 |
|
| 2013 |
Cortes-Ciriano I, Koutsoukas A, Abian O, Glen RC, Velazquez-Campoy A, Bender A. Experimental validation of in silico target predictions on synergistic protein targets Medchemcomm. 4: 278-288. DOI: 10.1039/C2Md20286G |
0.658 |
|
| 2012 |
Beale TM, Allwood DM, Bender A, Bond PJ, Brenton JD, Charnock-Jones DS, Ley SV, Myers RM, Shearman JW, Temple J, Unger J, Watts CA, Xian J. A-ring dihalogenation increases the cellular activity of combretastatin-templated tetrazoles. Acs Medicinal Chemistry Letters. 3: 177-81. PMID 24900453 DOI: 10.1021/Ml200149G |
0.351 |
|
| 2012 |
Rahmani H, Blockeel H, Bender A. Predicting genes involved in human cancer using network contextual information. Journal of Integrative Bioinformatics. 9: 210. PMID 22948007 DOI: 10.2390/Biecoll-Jib-2012-210 |
0.329 |
|
| 2012 |
O'Connell KM, Beckmann HS, Laraia L, Horsley HT, Bender A, Venkitaraman AR, Spring DR. A two-directional strategy for the diversity-oriented synthesis of macrocyclic scaffolds. Organic & Biomolecular Chemistry. 10: 7545-51. PMID 22890306 DOI: 10.1039/C2Ob26272J |
0.401 |
|
| 2012 |
van Westen GJ, van den Hoven OO, van der Pijl R, Mulder-Krieger T, de Vries H, Wegner JK, Ijzerman AP, van Vlijmen HW, Bender A. Identifying novel adenosine receptor ligands by simultaneous proteochemometric modeling of rat and human bioactivity data. Journal of Medicinal Chemistry. 55: 7010-20. PMID 22827545 DOI: 10.1021/Jm3003069 |
0.802 |
|
| 2012 |
van der Horst E, Marqués-Gallego P, Mulder-Krieger T, van Veldhoven J, Kruisselbrink J, Aleman A, Emmerich MT, Brussee J, Bender A, Ijzerman AP. Multi-objective evolutionary design of adenosine receptor ligands. Journal of Chemical Information and Modeling. 52: 1713-21. PMID 22647079 DOI: 10.1021/Ci2005115 |
0.54 |
|
| 2012 |
Sanders MP, Roumen L, van der Horst E, Lane JR, Vischer HF, van Offenbeek J, de Vries H, Verhoeven S, Chow KY, Verkaar F, Beukers MW, McGuire R, Leurs R, Ijzerman AP, de Vlieg J, ... ... Bender A, et al. A prospective cross-screening study on G-protein-coupled receptors: lessons learned in virtual compound library design. Journal of Medicinal Chemistry. 55: 5311-25. PMID 22563707 DOI: 10.1021/Jm300280E |
0.576 |
|
| 2012 |
Scior T, Bender A, Tresadern G, Medina-Franco JL, Martínez-Mayorga K, Langer T, Cuanalo-Contreras K, Agrafiotis DK. Recognizing pitfalls in virtual screening: a critical review. Journal of Chemical Information and Modeling. 52: 867-81. PMID 22435959 DOI: 10.1021/Ci200528D |
0.43 |
|
| 2012 |
Kirchmair J, Williamson MJ, Tyzack JD, Tan L, Bond PJ, Bender A, Glen RC. Computational prediction of metabolism: sites, products, SAR, P450 enzyme dynamics, and mechanisms. Journal of Chemical Information and Modeling. 52: 617-48. PMID 22339582 DOI: 10.1021/Ci200542M |
0.587 |
|
| 2012 |
Gleeson MP, Modi S, Bender A, Robinson RL, Kirchmair J, Promkatkaew M, Hannongbua S, Glen RC. The challenges involved in modeling toxicity data in silico: a review. Current Pharmaceutical Design. 18: 1266-91. PMID 22316153 DOI: 10.2174/138920012799362819 |
0.632 |
|
| 2012 |
Roessler FD, Korb O, Bender A, Maentele W, Bond PJ. Molecular dynamics simulations and docking of non-nucleoside reverse transcriptase inhibitors (NNRTIs): a possible approach to personalized HIV treatment Journal of Cheminformatics. 4: 32. DOI: 10.1186/1758-2946-4-S1-P32 |
0.367 |
|
| 2012 |
Bender A. Utilizing traditional Chinese for the discovery of efficacious new drugs Journal of Translational Medicine. 10: 1-1. DOI: 10.1186/1479-5876-10-S2-A34 |
0.371 |
|
| 2012 |
Wegner JK, Sterling A, Guha R, Bender A, Faulon JL, Hastings J, O'Boyle N, Overington J, Van Vlijmen H, Willighagen E. Cheminformatics Communications of the Acm. 55: 65-75. DOI: 10.1145/2366316.2366334 |
0.527 |
|
| 2011 |
Peironcely JE, Reijmers T, Coulier L, Bender A, Hankemeier T. Understanding and Classifying Metabolite Space and Metabolite-Likeness Plos One. 6. PMID 22194963 DOI: 10.1371/Journal.Pone.0028966 |
0.364 |
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| 2011 |
van Westen GJ, Wegner JK, Geluykens P, Kwanten L, Vereycken I, Peeters A, Ijzerman AP, van Vlijmen HW, Bender A. Which compound to select in lead optimization? Prospectively validated proteochemometric models guide preclinical development. Plos One. 6: e27518. PMID 22132107 DOI: 10.1371/Journal.Pone.0027518 |
0.813 |
|
| 2011 |
van der Horst E, van der Pijl R, Mulder-Krieger T, Bender A, Ijzerman AP. Substructure-based virtual screening for adenosine A2A receptor ligands. Chemmedchem. 6: 2302-11. PMID 22021213 DOI: 10.1002/Cmdc.201100369 |
0.545 |
|
| 2011 |
Bajorath J, Barreca ML, Bender A, Bryce R, Hutter M, Laggner C, Laughton C, Martin Y, Mitchell J, Padova A, Renner S, Selzer PM, Sherman W, Sippl W, Taft C, et al. Ask the experts: focus on computational chemistry. Future Medicinal Chemistry. 3: 909-921. PMID 21707395 DOI: 10.4155/Fmc.11.57 |
0.369 |
|
| 2011 |
Sushko I, Novotarskyi S, Körner R, Pandey AK, Rupp M, Teetz W, Brandmaier S, Abdelaziz A, Prokopenko VV, Tanchuk VY, Todeschini R, Varnek A, Marcou G, Ertl P, Potemkin V, ... ... Bender A, et al. Online chemical modeling environment (OCHEM): web platform for data storage, model development and publishing of chemical information. Journal of Computer-Aided Molecular Design. 25: 533-54. PMID 21660515 DOI: 10.1186/1758-2946-3-S1-P20 |
0.331 |
|
| 2011 |
Koutsoukas A, Simms B, Kirchmair J, Bond PJ, Whitmore AV, Zimmer S, Young MP, Jenkins JL, Glick M, Glen RC, Bender A. From in silico target prediction to multi-target drug design: current databases, methods and applications. Journal of Proteomics. 74: 2554-74. PMID 21621023 DOI: 10.1016/J.Jprot.2011.05.011 |
0.649 |
|
| 2011 |
Wang Z, Chen Y, Liang H, Bender A, Glen RC, Yan A. P-glycoprotein substrate models using support vector machines based on a comprehensive data set. Journal of Chemical Information and Modeling. 51: 1447-56. PMID 21604677 DOI: 10.1021/Ci2001583 |
0.593 |
|
| 2011 |
van der Horst E, Peironcely JE, van Westen GJ, van den Hoven OO, Galloway WR, Spring DR, Wegner JK, van Vlijmen HW, Ijzerman AP, Overington JP, Bender A. Chemogenomics approaches for receptor deorphanization and extensions of the chemogenomics concept to phenotypic space. Current Topics in Medicinal Chemistry. 11: 1964-77. PMID 21470175 DOI: 10.2174/156802611796391230 |
0.801 |
|
| 2011 |
Isidro-Llobet A, Murillo T, Bello P, Cilibrizzi A, Hodgkinson JT, Galloway WR, Bender A, Welch M, Spring DR. Diversity-oriented synthesis of macrocyclic peptidomimetics. Proceedings of the National Academy of Sciences of the United States of America. 108: 6793-8. PMID 21383137 DOI: 10.1073/Pnas.1015267108 |
0.415 |
|
| 2011 |
López-Vallejo F, Nefzi A, Bender A, Owen JR, Nabney IT, Houghten RA, Medina-Franco JL. Increased Diversity of Libraries from Libraries: Chemoinformatic Analysis of Bis-Diazacyclic Libraries Chemical Biology and Drug Design. 77: 328-342. PMID 21294850 DOI: 10.1111/J.1747-0285.2011.01100.X |
0.38 |
|
| 2011 |
Bender A. Bayesian methods in virtual screening and chemical biology Methods in Molecular Biology (Clifton, N.J.). 672: 175-196. PMID 20838969 DOI: 10.1007/978-1-60761-839-3_7 |
0.388 |
|
| 2011 |
Van Westen GJP, Wegner JK, Ijzerman AP, Van Vlijmen HWT, Bender A. Proteochemometric modeling as a tool to design selective compounds and for extrapolating to novel targets Medchemcomm. 2: 16-30. DOI: 10.1039/C0Md00165A |
0.596 |
|
| 2010 |
Bender A. How similar are those molecules after all? Use two descriptors and you will have three different answers. Expert Opinion On Drug Discovery. 5: 1141-1151. PMID 22822717 DOI: 10.1517/17460441.2010.517832 |
0.36 |
|
| 2010 |
van der Horst E, Peironcely JE, Ijzerman AP, Beukers MW, Lane JR, van Vlijmen HW, Emmerich MT, Okuno Y, Bender A. A novel chemogenomics analysis of G protein-coupled receptors (GPCRs) and their ligands: a potential strategy for receptor de-orphanization. Bmc Bioinformatics. 11: 316. PMID 20537162 DOI: 10.1186/1471-2105-11-316 |
0.706 |
|
| 2010 |
Yongye AB, Bender A, Martínez-Mayorga K. Dynamic clustering threshold reduces conformer ensemble size while maintaining a biologically relevant ensemble. Journal of Computer-Aided Molecular Design. 24: 675-686. PMID 20499135 DOI: 10.1007/S10822-010-9365-1 |
0.341 |
|
| 2010 |
Doddareddy MR, Klaasse EC, Shagufta, Ijzerman AP, Bender A. Prospective validation of a comprehensive in silico hERG model and its applications to commercial compound and drug databases. Chemmedchem. 5: 716-29. PMID 20349498 DOI: 10.1002/Cmdc.201000024 |
0.585 |
|
| 2010 |
van Westen GJ, Wegner JK, Bender A, Ijzerman AP, van Vlijmen HW. Mining protein dynamics from sets of crystal structures using "consensus structures". Protein Science : a Publication of the Protein Society. 19: 742-52. PMID 20120021 DOI: 10.1002/Pro.350 |
0.778 |
|
| 2010 |
van der Eelke H, Kruisselbrink J, Aleman A, Emmerich M, Bender A, IJzerman A. Evolutionary design of selective adenosine receptor ligands Journal of Cheminformatics. 2. DOI: 10.1186/1758-2946-2-S1-P48 |
0.559 |
|
| 2010 |
Peironcely JE, Bender A, Rojas-Chertó M, Reijmers TH, Coulier L, Hankemeier T. Expanding and understanding metabolite space Journal of Cheminformatics. 2: 39. DOI: 10.1186/1758-2946-2-S1-P39 |
0.339 |
|
| 2010 |
Hoven Ovd, Westen GJPv, Bender A. Predicting the binding type of compounds on the 4 adenosine receptors using proteochemometric models Journal of Cheminformatics. 2: 16. DOI: 10.1186/1758-2946-2-S1-P16 |
0.398 |
|
| 2010 |
Van Westen GJ, Wegner J, IJzerman A, Van Vlijmen H, Bender A. Molecular bioactivity extrapolation to novel targets by support vector machines Journal of Cheminformatics. 2. DOI: 10.1186/1758-2946-2-S1-O3 |
0.628 |
|
| 2010 |
Bender A. Compound bioactivities go public Nature Chemical Biology. 6: 309-309. DOI: 10.1038/Nchembio.354 |
0.33 |
|
| 2009 |
Kümmel A, Gabriel D, Parker CN, Bender A. Computational methods to support high-content screening: from compound selection and data analysis to postulating target hypotheses. Expert Opinion On Drug Discovery. 4: 5-13. PMID 23480331 DOI: 10.1517/17460440802586434 |
0.39 |
|
| 2009 |
Feng Y, Mitchison TJ, Bender A, Young DW, Tallarico JA. Multi-parameter phenotypic profiling: using cellular effects to characterize small-molecule compounds. Nature Reviews. Drug Discovery. 8: 567-78. PMID 19568283 DOI: 10.1038/Nrd2876 |
0.375 |
|
| 2009 |
Galloway WR, Bender A, Welch M, Spring DR. The discovery of antibacterial agents using diversity-oriented synthesis. Chemical Communications (Cambridge, England). 2446-62. PMID 19532856 DOI: 10.1039/B816852K |
0.369 |
|
| 2009 |
Sukuru SC, Jenkins JL, Beckwith RE, Scheiber J, Bender A, Mikhailov D, Davies JW, Glick M. Plate-based diversity selection based on empirical HTS data to enhance the number of hits and their chemical diversity. Journal of Biomolecular Screening. 14: 690-9. PMID 19531667 DOI: 10.1177/1087057109335678 |
0.422 |
|
| 2009 |
Medina-Franco JL, Martínez-Mayorga K, Bender A, Marín RM, Giulianotti MA, Pinilla C, Houghten RA. Characterization of activity landscapes using 2D and 3D similarity methods: consensus activity cliffs. Journal of Chemical Information and Modeling. 49: 477-91. PMID 19434846 DOI: 10.1021/Ci800379Q |
0.367 |
|
| 2009 |
van der Horst E, Okuno Y, Bender A, IJzerman AP. Substructure mining of GPCR ligands reveals activity-class specific functional groups in an unbiased manner. Journal of Chemical Information and Modeling. 49: 348-60. PMID 19434836 DOI: 10.1021/Ci8003896 |
0.532 |
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| 2009 |
Scheiber J, Chen B, Milik M, Sukuru SC, Bender A, Mikhailov D, Whitebread S, Hamon J, Azzaoui K, Urban L, Glick M, Davies JW, Jenkins JL. Gaining insight into off-target mediated effects of drug candidates with a comprehensive systems chemical biology analysis. Journal of Chemical Information and Modeling. 49: 308-17. PMID 19434832 DOI: 10.1021/Ci800344P |
0.448 |
|
| 2009 |
Scheiber J, Jenkins JL, Sukuru SC, Bender A, Mikhailov D, Milik M, Azzaoui K, Whitebread S, Hamon J, Urban L, Glick M, Davies JW. Mapping adverse drug reactions in chemical space. Journal of Medicinal Chemistry. 52: 3103-7. PMID 19378990 DOI: 10.1021/Jm801546K |
0.307 |
|
| 2009 |
Prathipati P, Ma NL, Manjunatha UH, Bender A. Fishing the Target of Antitubercular Compounds: In Silico Target Deconvolution Model Development and Validation Journal of Proteome Research. 8: 2788-2798. PMID 19301903 DOI: 10.1021/Pr8010843 |
0.465 |
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| 2009 |
Bender A, Mikhailov D, Glick M, Scheiber J, Davies JW, Cleaver S, Marshall S, Tallarico JA, Harrington E, Cornella-Taracido I, Jenkins JL. Use of ligand based models for protein domains to predict novel molecular targets and applications to triage affinity chromatography data. Journal of Proteome Research. 8: 2575-85. PMID 19271732 DOI: 10.1021/Pr900107Z |
0.46 |
|
| 2009 |
Bender A, Jenkins JL, Scheiber J, Sukuru SC, Glick M, Davies JW. How similar are similarity searching methods? A principal component analysis of molecular descriptor space. Journal of Chemical Information and Modeling. 49: 108-19. PMID 19123924 DOI: 10.1021/Ci800249S |
0.412 |
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| 2009 |
Horst EVD, Bender A, Ijzerman AP. Frequent substructure mining of GPCR ligands Chemistry Central Journal. 3. DOI: 10.1186/1752-153X-3-S1-P69 |
0.476 |
|
| 2009 |
Emmerich M, Lee B, Bender A, Faddiev E, Kruisselbrink J, Deutz A, Horst Evd, IJzerman A, Bäck T. Analyzing molecular landscapes using random walks and information theory Chemistry Central Journal. 3. DOI: 10.1186/1752-153X-3-S1-P20 |
0.528 |
|
| 2009 |
Doddareddy MR, van Westen GJP, van der Horst E, Peironcely JE, Corthals F, Ijzerman AP, Emmerich M, Jenkins JL, Bender A. Chemogenomics: Looking at biology through the lens of chemistry Statistical Analysis and Data Mining. 2: 149-160. DOI: 10.1002/Sam.V2:3 |
0.498 |
|
| 2009 |
Scheiber J, Jenkins JL, Bender A, Milik M, Mikhailov D, Sukuru SCK, Cornett B, Whitebread S, Urban L, Davies JW, Glick M. SPREAD—exploiting chemical features that cause differential activity behavior Statistical Analysis and Data Mining. 2: 115-122. DOI: 10.1002/Sam.V2:2 |
0.405 |
|
| 2009 |
Scheiber J, Jenkins JL, Bender A, Milik M, Mikhailov D, Sukuru SCK, Cornett B, Whitebread S, Urban L, Davies JW, Glick M. SPREAD-exploiting chemical features that cause differential activity behavior Statistical Analysis and Data Mining. 2: 115-122. DOI: 10.1002/Sam.10036 |
0.4 |
|
| 2009 |
Medina‐Franco JL, Martínez‐Mayorga K, Bender A, Scior T. Scaffold Diversity Analysis of Compound Data Sets Using an Entropy-Based Measure Qsar & Combinatorial Science. 28: 1551-1560. DOI: 10.1002/Qsar.200960069 |
0.414 |
|
| 2008 |
Nigsch F, Bender A, Jenkins JL, Mitchell JB. Ligand-target prediction using Winnow and naive Bayesian algorithms and the implications of overall performance statistics. Journal of Chemical Information and Modeling. 48: 2313-25. PMID 19055411 DOI: 10.1021/Ci800079X |
0.424 |
|
| 2008 |
Karthikeyan M, Krishnan S, Pandey AK, Bender A, Tropsha A. Distributed chemical computing using ChemStar: an open source java remote method invocation architecture applied to large scale molecular data from PubChem. Journal of Chemical Information and Modeling. 48: 691-703. PMID 18402434 DOI: 10.1021/Ci700334F |
0.307 |
|
| 2008 |
Spandl RJ, Bender A, Spring DR. Diversity-oriented synthesis; a spectrum of approaches and results. Organic & Biomolecular Chemistry. 6: 1149-58. PMID 18362950 DOI: 10.1039/B719372F |
0.362 |
|
| 2008 |
Crisman TJ, Bender A, Milik M, Jenkins JL, Scheiber J, Sukuru SC, Fejzo J, Hommel U, Davies JW, Glick M. "Virtual fragment linking": an approach to identify potent binders from low affinity fragment hits. Journal of Medicinal Chemistry. 51: 2481-91. PMID 18357974 DOI: 10.1021/Jm701314U |
0.404 |
|
| 2008 |
Thomas GL, Spandl RJ, Glansdorp FG, Welch M, Bender A, Cockfield J, Lindsay JA, Bryant C, Brown DF, Loiseleur O, Rudyk H, Ladlow M, Spring DR. Anti-MRSA agent discovery using diversity-oriented synthesis. Angewandte Chemie (International Ed. in English). 47: 2808-12. PMID 18307176 DOI: 10.1002/Anie.200705415 |
0.328 |
|
| 2008 |
Young DW, Bender A, Hoyt J, McWhinnie E, Chirn GW, Tao CY, Tallarico JA, Labow M, Jenkins JL, Mitchison TJ, Feng Y. Integrating high-content screening and ligand-target prediction to identify mechanism of action. Nature Chemical Biology. 4: 59-68. PMID 18066055 DOI: 10.1038/Nchembio.2007.53 |
0.453 |
|
| 2008 |
Scheiber J, Jenkins J, Bender A, Whitebread S, Hamon J, Urban L, Azzaoui K, Glick M, Davies J. Side effect profile prediction - early addressing of big pharma's worst nightmare Chemistry Central Journal. 2: 1-1. DOI: 10.1186/1752-153X-2-S1-S4 |
0.435 |
|
| 2007 |
Bender A, Young DW, Jenkins JL, Serrano M, Mikhailov D, Clemons PA, Davies JW. Chemogenomic data analysis: prediction of small-molecule targets and the advent of biological fingerprint. Combinatorial Chemistry & High Throughput Screening. 10: 719-31. PMID 18045083 DOI: 10.2174/138620707782507313 |
0.47 |
|
| 2007 |
Li Q, Bender A, Pei J, Lai L. A large descriptor set and a probabilistic kernel-based classifier significantly improve druglikeness classification. Journal of Chemical Information and Modeling. 47: 1776-86. PMID 17718552 DOI: 10.1021/Ci700107Y |
0.379 |
|
| 2007 |
Crisman TJ, Parker CN, Jenkins JL, Scheiber J, Thoma M, Kang ZB, Kim R, Bender A, Nettles JH, Davies JW, Glick M. Understanding false positives in reporter gene assays: in silico chemogenomics approaches to prioritize cell-based HTS data. Journal of Chemical Information and Modeling. 47: 1319-27. PMID 17608469 DOI: 10.1021/Ci6005504 |
0.451 |
|
| 2007 |
Azzaoui K, Hamon J, Faller B, Whitebread S, Jacoby E, Bender A, Jenkins JL, Urban L. Modeling promiscuity based on in vitro safety pharmacology profiling data. Chemmedchem. 2: 874-80. PMID 17492703 DOI: 10.1002/Cmdc.200700036 |
0.445 |
|
| 2007 |
Bender A, Scheiber J, Glick M, Davies JW, Azzaoui K, Hamon J, Urban L, Whitebread S, Jenkins JL. Analysis of pharmacology data and the prediction of adverse drug reactions and off-target effects from chemical structure. Chemmedchem. 2: 861-73. PMID 17477341 DOI: 10.1002/Cmdc.200700026 |
0.402 |
|
| 2007 |
Crisman TJ, Jenkins JL, Parker CN, Hill WA, Bender A, Deng Z, Nettles JH, Davies JW, Glick M. "Plate cherry picking": a novel semi-sequential screening paradigm for cheaper, faster, information-rich compound selection. Journal of Biomolecular Screening. 12: 320-7. PMID 17438067 DOI: 10.1177/1087057107299427 |
0.421 |
|
| 2007 |
Nettles JH, Jenkins JL, Williams C, Clark AM, Bender A, Deng Z, Davies JW, Glick M. Flexible 3D pharmacophores as descriptors of dynamic biological space. Journal of Molecular Graphics & Modelling. 26: 622-33. PMID 17395510 DOI: 10.1016/J.Jmgm.2007.02.005 |
0.409 |
|
| 2007 |
Cannon EO, Amini A, Bender A, Sternberg MJ, Muggleton SH, Glen RC, Mitchell JB. 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. 21: 269-80. PMID 17387437 DOI: 10.1007/S10822-007-9113-3 |
0.584 |
|
| 2007 |
Bender A, Scheiber J, Glick M, Davies J, Azzaoui K, Hamon J, Urban L, Whitebread S, Jenkins J. Cover Picture: Analysis of Pharmacology Data and the Prediction of Adverse Drug Reactions and Off-Target Effects from Chemical Structure (ChemMedChem 6/2007) Chemmedchem. 2: 733-733. DOI: 10.1002/Cmdc.200790016 |
0.371 |
|
| 2006 |
Bender A, Jenkins JL, Li Q, Adams SE, Cannon EO, Glen RC. Chapter 9 Molecular Similarity: Advances in Methods, Applications and Validations in Virtual Screening and QSAR. Annual Reports in Computational Chemistry. 2: 141-168. PMID 32362803 DOI: 10.1016/S1574-1400(06)02009-3 |
0.613 |
|
| 2006 |
Nettles JH, Jenkins JL, Bender A, Deng Z, Davies JW, Glick M. Bridging chemical and biological space: "target fishing" using 2D and 3D molecular descriptors. Journal of Medicinal Chemistry. 49: 6802-10. PMID 17154510 DOI: 10.1021/Jm060902W |
0.402 |
|
| 2006 |
Bender A, Jenkins JL, Glick M, Deng Z, Nettles JH, Davies JW. "Bayes affinity fingerprints" improve retrieval rates in virtual screening and define orthogonal bioactivity space: when are multitarget drugs a feasible concept? Journal of Chemical Information and Modeling. 46: 2445-56. PMID 17125186 DOI: 10.1021/Ci600197Y |
0.401 |
|
| 2006 |
Nigsch F, Bender A, van Buuren B, Tissen J, Nigsch E, Mitchell JB. Melting point prediction employing k-nearest neighbor algorithms and genetic parameter optimization. Journal of Chemical Information and Modeling. 46: 2412-22. PMID 17125183 DOI: 10.1021/Ci060149F |
0.353 |
|
| 2006 |
Cannon EO, Bender A, Palmer DS, Mitchell JB. Chemoinformatics-based classification of prohibited substances employed for doping in sport. Journal of Chemical Information and Modeling. 46: 2369-80. PMID 17125180 DOI: 10.1021/Ci0601160 |
0.367 |
|
| 2006 |
Wyatt EE, Fergus S, Galloway WR, Bender A, Fox DJ, Plowright AT, Jessiman AS, Welch M, Spring DR. Skeletal diversity construction via a branching synthetic strategy. Chemical Communications (Cambridge, England). 3296-8. PMID 16883415 DOI: 10.1039/B607710B |
0.312 |
|
| 2006 |
Givehchi A, Bender A, Glen RC. Analysis of activity space by fragment fingerprints, 2D descriptors, and multitarget dependent transformation of 2D descriptors. Journal of Chemical Information and Modeling. 46: 1078-83. PMID 16711727 DOI: 10.1021/Ci0500233 |
0.56 |
|
| 2006 |
Rodgers S, Glen RC, Bender A. Characterizing bitterness: identification of key structural features and development of a classification model. Journal of Chemical Information and Modeling. 46: 569-76. PMID 16562985 DOI: 10.1021/Ci0504418 |
0.623 |
|
| 2006 |
Karthikeyan M, Krishnan S, Pandey AK, Bender A. Harvesting chemical information from the internet using a distributed approach: ChemXtreme Journal of Chemical Information and Modeling. 46: 452-461. PMID 16562972 DOI: 10.1021/Ci050329+ |
0.308 |
|
| 2006 |
Bender A, Jenkins JL, Li Q, Adams SE, Cannon EO, Glen RC. Chapter 9 Molecular Similarity: Advances in Methods, Applications and Validations in Virtual Screening and QSAR Annual Reports in Computational Chemistry. 2: 141-168. DOI: 10.1016/S1574-1400(06)02009-3 |
0.519 |
|
| 2006 |
Jenkins JL, Bender A, Davies JW. In silico target fishing: Predicting biological targets from chemical structure Drug Discovery Today: Technologies. 3: 413-421. DOI: 10.1016/J.Ddtec.2006.12.008 |
0.428 |
|
| 2005 |
Bender A, Glen RC. 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. 45: 1369-75. PMID 16180913 DOI: 10.1021/Ci0500177 |
0.635 |
|
| 2005 |
Bender A, Mussa HY, Glen RC. 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 balanced chemistry in training and test sets. Journal of Biomolecular Screening. 10: 658-66. PMID 16170051 DOI: 10.1177/1087057105281048 |
0.579 |
|
| 2005 |
Fergus S, Bender A, Spring DR. Assessment of structural diversity in combinatorial synthesis. Current Opinion in Chemical Biology. 9: 304-9. PMID 15939333 DOI: 10.1016/J.Cbpa.2005.03.004 |
0.359 |
|
| 2005 |
Karthikeyan M, Glen RC, Bender A. General melting point prediction based on a diverse compound data set and artificial neural networks. Journal of Chemical Information and Modeling. 45: 581-90. PMID 15921448 DOI: 10.1021/Ci0500132 |
0.625 |
|
| 2005 |
Bender A, Klamt A, Wichmann K, Thormann M, Glen RC. Molecular similarity searching using COSMO screening charges (COSMO/3PP) Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 3695: 175-185. DOI: 10.1007/11560500_16 |
0.633 |
|
| 2004 |
Bender A, Mussa HY, Gill GS, Glen RC. Molecular surface point environments for virtual screening and the elucidation of binding patterns (MOLPRINT 3D). Journal of Medicinal Chemistry. 47: 6569-83. PMID 15588092 DOI: 10.1021/jm049611i |
0.552 |
|
| 2004 |
Bender A, Glen RC. Molecular similarity: a key technique in molecular informatics. Organic & Biomolecular Chemistry. 2: 3204-18. PMID 15534697 DOI: 10.1039/B409813G |
0.632 |
|
| 2004 |
Bender A, Mussa HY, Glen RC, Reiling S. Similarity searching of chemical databases using atom environment descriptors (MOLPRINT 2D): evaluation of performance. Journal of Chemical Information and Computer Sciences. 44: 1708-18. PMID 15446830 DOI: 10.1021/Ci0498719 |
0.597 |
|
| 2004 |
Bender A, Mussa HY, Glen RC, Reiling S. Molecular similarity searching using atom environments, information-based feature selection, and a naïve Bayesian classifier. Journal of Chemical Information and Computer Sciences. 44: 170-8. PMID 14741025 DOI: 10.1021/Ci034207Y |
0.609 |
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