| Scientific Articles | Reference | Link |
 84. Understanding and Classifying Metabolite Space and Metabolite-Likeness. read article (online from 14 December 2011) Julio E. Peironcely, Theo Reijmers, Leon Coulier, Andreas Bender and Thomas Hankemeier. | PLoS One 2011 e28966. | DOI: 10.1371/journal.pone.0028966 (valid from 14 December 2011) Request PDF Reprint |
83. Which Compound to Select in Lead Optimization? Prospectively Validated Proteochemometric Models Guide Preclinical Development. read article Gerard J.P. van Westen, Jörg K. Wegner, Peggy Geluykens, Leen Kwanten, Inge Vereycken, Anik Peeters, Adriaan P. IJzerman, Herman W.T. van Vlijmen and Andreas Bender. | PLoS One 2011 (6) e27518. | DOI: 10.1371/journal.pone.0027518 Request PDF Reprint |
82. The challenges involved in Modeling Toxicity Data in silico: A Review. read article M. Paul Gleeson, Sandeep Modi, Andreas Bender, Richard L. Marchese Robinson, Johannes Kirchmair, Malinee Promkatkaew, Supa Hannongbua and Robert C. Glen. | Curr. Pharm. Des. 2011 (in press). | DOI: not yet Request PDF Reprint |
81. Substructure-Based Virtual Screening for Adenosine A2A Receptor Ligands. read article Eelke van der Horst, Rianne van der Pijl, Thea Mulder-Krieger, Andreas Bender, and Adriaan P. IJzerman. | ChemMedChem 2011 (12) 2302 - 2311. | DOI: 10.1073/10.1002/cmdc.201100369 Request PDF Reprint |
80. Collaboration-based Function Prediction in Protein-Protein Interaction Networks. read article Hossein Rahmahi, Hendrik Blockeel and Andreas Bender. | Proc. IDA (Lect. Notes Comput. Sci.) 2011 (7014) 318 - 327. | DOI: 10.1007/978-3-642-24800-9_30 Request PDF Reprint |
79. Interaction-Based Feature Selection for Predicting Cancer-Related Proteins in Protein-Protein Interaction Networks. read article Hossein Rahmahi, Hendrik Blockeel and Andreas Bender. | Proc. 5th Int. Workshop in Machine Learn. Syst. Biol. (MLSB11) 2011. | DOI: https://lirias.kuleuven.be/bitstream/123456789/310757/1/MLSB2011.pdf Request PDF Reprint |
78. From in silico target prediction to multi-target drug design: Current databases, methods and applications. read article Alexios Koutsoukas, Benjamin Simms, Johannes Kirchmair, Peter J. Bond, Alan V. Whitmore, Steven Zimmer, Malcolm P. Young, Jeremy L. Jenkins, Meir Glick, Robert C. Glen and Andreas Bender. | J. Proteomics 2011 (74) 2554 - 2574. | DOI: 10.1073/10.1016/j.jprot.2011.05.011 Request PDF Reprint |
77. Online Chemical Modeling Environment (OCHEM): Web Platform for Data Storage, Model Development and Publishing of Chemical Information. read article Iurii Sushko, Sergii Novotarskyi, Robert Körner, Anil Kumar Pandey, Matthias Rupp, Wolfram Teetz, Stefan Brandmaier, Ahmed Abdelaziz, Volodymyr V. Prokopenko, Vsevolod Y. Tanchuk, Roberto Todeschini, Alexander Varnek, Gilles Marcou, Peter Ertl, Vladimir Potemkin, Maria Grishina, Johann Gasteiger, Christof Schwab, Igor I. Baskin, Vladimir A. Palyulin, Eugene V. Radchenko, William J. Welsh, Vladyslav Kholodovych, Dmitriy Chekmarev, Artem Cherkasov, Joao Aires-de-Sousa, Qing-You Zhang, Andreas Bender, Florian Nigsch, Luc Patiny, Antony Williams, Valery Tkachenko and Igor V. Tetko | J. Comput.-Aided Mol. Des. 2011 (25) 533 - 554. | DOI: 10.1007/s10822-011-9440-2 Request PDF Reprint |
76. P-glycoprotein Substrate Models Using Support Vector Machines Based on a Comprehensive Dataset. read article Zhi Wang, Yuanying Chen, Hu Liang, Andreas Bender, Robert Glen and Aixia Yan. | J. Chem./ Inf. Model 2011 (51) 1447 - 1456. | DOI: 10.1021/ci2001583 Request PDF Reprint |
75. Efficient calculation of compound similarity based on maximum common subgraphs and its application to prediction of gene transcript levels. Rogier J.P. van Berlo, Marco J.L. de Groot, Andreas Bender, Peter J.T. Verheijen, Marcel J.T. Reinders and Dick de Ridder. | Int. J. Bioinf. Res. Appl. 2011 (in press). | DOI: not yet Request PDF Reprint |
74. Diversity-oriented synthesis of macrocyclic peptidomimetics. read article Albert Isidro-Llobet, Tiffanie Murillo, Paula Bello, Agostino Cilibrizzia, James T. Hodgkinson, Warren R. J. D. Galloway, Andreas Bender, Martin Welch and David R. Spring. | Proc. Natl. Acad. Sci. USA 2011 (108) 6793 - 6798. | DOI: 10.1073/pnas.1015267108 Request PDF Reprint |
73. Increased Diversity of Libraries from Libraries: Chemoinformatic Analysis of Bis-Diazacyclic Libraries. read article Fabian Lopez-Vallejo, Adel Nefzi, Andreas Bender, John R. Owen, Ian T. Nabney, Richard A. Houghten and Jose L. Medina-Franco. | Chem. Biol. Drug Des. 2011 (77) 328 - 342. | DOI: 10.1111/j.1747-0285.2011.01100.x Request PDF Reprint |
72. Chemogenomics Approaches for Receptor Deorphanization and Extensions of the Chemogenomics Concept to Phenotypic Space. read article Eelke van der Horst, Julio E. Peironcely, Gerard J. P. van Westen, Olaf O. van den Hoven, Warren R. J. D. Galloway, David R. Spring, Joerg K. Wegner, Herman W. T. van Vlijmen, Ad P. IJzerman, John P. Overington and Andreas Bender. | Curr. Top. Med. Chem 2011 (11) 1964 - 1977. | DOI: 10.2174/156802611796391230 Request PDF Reprint |
71. Proteochemometric modeling as a tool to design selective compounds and for extrapolating to novel targets. read article Gerard J. P. van Westen, Joerg K. Wegner, Adriaan P. IJzerman, Herman W. T. van Vlijmen and Andreas Bender. | MedChemComm 2011 (2) 16 - 30. | DOI: 10.1039/C0MD00165A Request PDF Reprint |
70. Bayesian Methods in Virtual Screening and Chemical Biology. read article Andreas Bender. | In: Bayesian Methods in Virtual Screening and Chemical Biology, Jurgen Bajorath (Ed.), Meth. Mol. Biol., 2011 (672) 175 - 196. | DOI: 10.1007/978-1-60761-839-3_7 Request PDF Reprint |
69. How similar are those molecules after all? Use two descriptors and you will have three different answers. read article Andreas Bender. | Exp. Op. Drug Discov. 2010 (5) 1141 - 1151. | DOI: 10.1517/17460441.2010.517832 Request PDF Reprint |
68. Virtual Activity Profiling of Bioactive Molecules by 1D Fingerprinting. read article Aimy Sebastian, Andreas Bender and Vibin Ramakrishnan. | Mol. Inf. 2010 (29) 773 - 779. | DOI: 10.1002/minf.201000075 Request PDF Reprint |
67. Collaboration-based Function Prediction in Protein-Protein Interaction networks. read article Hossein Rahmani, Hendrik Blockeel and Andreas Bender. | In: Proc. 4th Int. Workshop in Machine Learn. Syst. Biol. (MLSB10) 2010 55 - 58. | DOI: N/A Request PDF Reprint |
66. A novel chemogenomics analysis of G protein coupled receptors (GPCRs) and their ligands: a potential strategy for receptor de-orphanization. read article Eelke van der Horst, Julio E. Peironcely, Adriaan P. IJzerman, Margot W. Beukers, J. Robert Lane, Herman W.T. van Vlijmen, Michael T.M. Emmerich, Yasushi Okuno and Andreas Bender. | BMC Bioinformatics 2010 (11) 316. | DOI: 10.1186/1471-2105-11-316 Request PDF Reprint |
65. Dynamic clustering threshold reduces conformer ensemble size while maintaining a biologically relevant ensemble. read article Austin B. Yongye, Andreas Bender and Karina Martinez-Mayorga. | J. Comp.-Aided Drug Des. 2010 (24) 675 - 686. | DOI: 10.1007/s10822-010-9365-1 Request PDF Reprint |
64. Prospective Validation of a Comprehensive In silico hERG model and its Applications to Commercial Compound and Drug Databases. read article The supplementary material of the article, containing 2600+ hERG data points with literature sources, can now also be downloaded from
this location.
Munikumar R. Doddareddy, Elisabeth C.Klaasse, Shagufta, Adriaan P. IJzerman and Andreas Bender. | ChemMedChem 2010 (5) 716 - 729. | DOI: 10.1002/cmdc.201000024 Request PDF Reprint |
63. Mining protein dynamics from sets of crystal structures using "consensus structures". read article Gerard J.P. van Westen, Jörg K. Wegner, Andreas Bender, Adriaan P. IJzerman and Herman W.T. van Vlijmen. | Protein Sci. 2010 (19) 742 - 752. | DOI: 10.1002/pro.350 Request PDF Reprint |
62. Predicting the functions of proteins in Protein-Protein Interaction networks from global information. read article Hossein Rahmani, Hendrik Blockeel and Andreas Bender. | J. Mach. Learn. Res. 2010 (8) 82 - 97. | DOI: Journal Article Request PDF Reprint |
61. Alpha Shapes Applied to Molecular Shape Characterization Exhibit Novel Properties Compared to Established Shape Descriptors. read article J. Anthony Wilson, Andreas Bender, Taner Kaya and Paul A. Clemons. | J. Chem. Inf. Model. 2009 (49) 2231 - 2241. | DOI: 10.1021/ci900190z Request PDF Reprint |
60. Scaffold Diversity Analysis of Compound Data Sets Using an Entropy-Based Measure. read article Jose L. Medina-Franco, Karina Martínez-Mayorga, Andreas Bender and Thomas Scior. | QSAR Comb. Sci. 2009 (11-12) 1551 - 1560. | DOI: 10.1002/qsar.200960069 Request PDF Reprint |
59. Predicting the functions of proteins in PPI networks from global information. read article Hossein Rahmani, Hendrik Blockeel, and Andreas Bender. | Proc. 3rd Int. Workshop in Machine Learn. Syst. Biol. (MLSB09), 2009 85-94. | DOI: http://mlsb09.ijs.si/files/MLSB09-Proceedings.pdf Request PDF Reprint |
58. Multi-parameter Phenotypic Profiling: Characterization of Small-molecule Compounds Based on Their Effects on Cells. read article Yan Feng, Timothy J. Mitchison, Andreas Bender, Daniel W. Young and John A. Tallarico. | Nature Rev. Drug Discov. 2009 (8) 567 - 578. | DOI: 10.1038/nrd2876 Request PDF Reprint |
57. Mapping Adverse Drug Reactions in Chemical Space. read article Josef Scheiber, Jeremy L. Jenkins, Sai Chetan K. Sukuru, Andreas Bender, Dmitri Mikhailov, Mariusz Milik, Kamal Azzaoui, Steven Whitebread, Jacques Hamon, Laszlo Urban, Meir Glick and John W. Davies. | J. Med. Chem. 2009 (52) 3103–3107. | DOI: 10.1021/jm801546k Request PDF Reprint |
56. Knowledge-based and computational approaches based on in vitro safety pharmacology. read article Josef Scheiber, Andreas Bender, Kamal Azzaoui and Jeremy Jenkins. | In: In: Hit and Lead Profiling, Wiley/VCH, Bernard Faller and Laszlo Urban (Ed.) 2009. | Book on Wiley-VCH Website Request PDF Reprint |
55. Enhancing Search Space Diversity in Multi-Objective Evolutionary Drug Molecule Design using Niching. Johannes W. Kruisselbrink, Alexander Aleman, Michael T. M. Emmerich, Ad P. IJzerman, Andreas Bender, Thomas Baeck and Eelke van der Horst. | Proc. Gen. Evol. Comput. Conf., GECCO-2009. 2009. | Request PDF Reprint |
54. Chemogenomics: Looking at Biology through the Lens of Chemistry. read article Munikumar R. Doddareddy, Gerard J. P. van Westen, Eelke van der Horst, Julio E. Peironcely, Frans Corthals, Adriaan P. IJzerman, Michael Emmerich, Jeremy L. Jenkins and Andreas Bender. | Stat. Anal. Data Mining 2009 (2) 149 - 160. | DOI: 10.1002/sam.10046 Request PDF Reprint |
53. Plate-Based Diversity Selection Based on Empirical HTS Data to Enhance the Number of Hits and Their Chemical Diversity. read article Sai Chetan K. Sukuru, Jeremy L. Jenkins, Rohan J. Beckwith, Josef Scheiber, Andreas Bender, Dmitri Mikhailov, John W. Davies and Meir Glick. | J. Biomol. Scr. 2009 (14) 690 - 699. | DOI: 10.1177/1087057109335678 Request PDF Reprint |
52. The discovery of antibacterial agents using diversity-oriented synthesis. read article Warren R. J. D. Galloway, Andreas Bender, Martin Welch and David R. Spring | Chem. Commun. 2009, 2446 - 2462. | DOI: 10.1039/b816852k Request PDF Reprint |
51. Fishing the target of Antitubercular Compounds: In silico target deconvolution model development and validation. read article Philip Prathipati, Ngai Ma, Ujjini Manjunatha and Andreas Bender. | J. Proteome Res. 2009 (8) 2788 - 2798 | DOI: 10.1021/pr8010843 Request PDF Reprint |
50. Use of Ligand Based Models for Protein Domains To Predict Novel Molecular Targets and Applications To Triage Affinity Chromatography Data read article Andreas Bender, Dmitri Mikhailov, Meir Glick, Josef Scheiber, John W. Davies, Stephen Cleaver, Stephen Marshall, John A. Tallarico, Edmund Harrington, Ivan Cornella-Taracido, and Jeremy L. Jenkins. | J. Proteome Res. 2009 (8) 2575 - 2585. | DOI: 10.1021/pr900107z Request PDF Reprint |
49. SPREAD – Exploiting chemical features that cause differential activity behaviour. read article Josef Scheiber, Jeremy L. Jenkins, Andreas Bender, Mariusz Milik, Dmitri Mikhailov, S. Chetan K. Sukuru, Ben Cornett, Steven Whitebread, Laszlo Urban, John W. Davies and Meir Glick. | Stat. Anal. Data Mining 2009 (2) 149 - 160. | DOI: not yet Request PDF Reprint |
48. Combining Aggregation with Pareto Optimization: A Case Study in Evolutionary Molecular Design. read article Johannes W. Kruisselbrink, Michael T.M. Emmerich, Thomas Back, Andreas Bender, Ad P. IJzerman and Eelke van der Horst. | Proceedings of EMO’09 (Lect. Notes Comput. Sci.) 2009 (5467) 453 - 467. | DOI: not yet Request PDF Reprint |
47. How Similar Are Similarity Searching Methods? A Principal Component Analysis of Molecular Descriptor Space read article Andreas Bender, Jeremy L. Jenkins, Josef Scheiber, Sai Chetan K. Sukuru, Meir Glick and John W. Davies. | J. Chem. Inf. Model 2009 (49) 108 - 119. | DOI: 10.1021/ci800249s Request PDF Reprint |
46. A Comprehensive Systems Chemical Biology Analysis Gains Insight into Off-Target Mediated Effects of Drug Candidates read article Josef Scheiber, Bin Chen, Mariusz Milik, Sai Chetan K. Sukuru, Andreas Bender, Dmitri Mikhailov, Steven Whitebread, Jacques Hamon, Kamal Azzaoui, Laszlo Urban, Meir Glick, John W. Davies and Jeremy L. Jenkins. | J. Chem. Inf. Model 2009 (49) 308 - 317. | DOI: 10.1021/ci800344p Request PDF Reprint |
45. Characterization of Activity Landscapes Using 2D and 3D Similarity Methods: Consensus Activity Cliffs read article Jose L. Medina-Franco, Karina Martínez-Mayorga, Andreas Bender, Ray M. Marín, Marc A. Giulianotti, Clemencia Pinilla and Richard A. Houghten. | J. Chem. Inf. Model 2009 (49) 477 - 491. | DOI: 10.1021/ci800379q Request PDF Reprint |
44. Substructure Mining of GPCR Ligands Reveals Activity-Class Specific Functional Groups in an Unbiased Manner read article Eelke van der Horst, Yasushi Okuno, Andreas Bender, and Adriaan P. IJzerman. | J. Chem. Inf. Model 2009 (49) 348 - 360. | DOI: 10.1021/ci8003896 Request PDF Reprint |
43. Computational Methods to Support High-Content Screening: From Compound Selection and Data Analysis to Postulating Target Hypotheses read article Anne Kümmel, Daniela Gabriel, Christian N. Parker and Andreas Bender. | Exp. Op. Drug Discov. 2009 (4) 5 - 13. | DOI: 10.1517/17460440802586434 Request PDF Reprint |
42. A Scenario Implementation in R for SubtypeDiscovery Examplified on Chemoinformatics Data read article Fabrice Colas, Ingrid Meulenbelt, Jeanine J. Houwing-Duistermaat, Margreet Kloppenburg, Iain Watt, Stephanie M. van Rooden, Martine Visser, Johan Marinus, Edward O. Cannon, Andreas Bender, Jacobus J. van Hilten, P. Eline Slagboom and Joost N. Kok. | Comm. Comp. Inf. Sci. 2009 (17) 669-683. | DOI: 10.1007/978-3-540-88479-8_48 PDF on conference website Request PDF Reprint |
41. Ligand-Target Prediction Using Winnow and Naive Bayesian Algorithms and the Implications of Overall Performance Statistics read article Florian Nigsch, Andreas Bender, Jeremy L. Jenkins and John B. O. Mitchell. | J. Chem. Inf. Model. 2008 2008 (48) 2313 – 2325. | DOI: 10.1021/ci800079x Request PDF Reprint |
40. A Quantitative bgl Operon Model for E. coli Requires BglF Conformational Change for Sugar Transport read article Paras Chopra and Andreas Bender | Trans. on Comput. Syst. Biol. 2008 (9) 1-22. | DOI: to be assigned Request PDF Reprint |
39. Which aspects of HTS are empirically correlated with downstream success? read article Andreas Bender, Dejan Bojanic, John W. Davies, Thomas J. Crisman, Dmitri Mikhailov, Josef Scheiber, Jeremy L. Jenkins, Zhan Deng, W. Adam G. Hill, Maxim Popov, Edgar Jacoby and Meir Glick | Curr. Opin. Drug Discov. Devel. 2008 (11) 327-337. | DOI: PDF on BioMedCentral Request PDF Reprint |
38. Distributed Chemical Computing Using ChemStar: An Open Source Java RMI Architecture applied to Large Scale Molecular Data from PubChem read article M. Karthikeyan, Anil Kumar Pandey, S. Krishnan, Andreas Bender and Alexander Tropsha. | J. Chem. Inf. Model. 2008 (48) 691 - 703. | DOI: 10.1021/ci700334f Request PDF Reprint |
37. "Virtual Fragment Linking": An Approach To Identify Potent Binders from Low Affinity Fragment Hits read article Thomas J. Crisman, Andreas Bender, Mariusz Milik, Jeremy L. Jenkins, Josef Scheiber, Sai Chetan K. Sukuru, Jasna Fejzo, Ulrich Hommel, John W. Davies, and Meir Glick | J. Med. Chem. 2008 (51) 2481 - 2491. | DOI: 10.1021/jm701314u Request PDF Reprint |
36. Anti-MRSA Agent Discovery Using Diversity-Oriented Synthesis read article Gemma L. Thomas, Richard J. Spandl, Freija G. Glansdorp, Martin Welch, Andreas Bender, Joshua Cockfield, Jodi A. Lindsay, Clare Bryant, Derek F. J. Brown, Olivier Loiseleur, Helene Rudyk, Mark Ladlow, and David R. Spring | Angew. Chem. Int. Ed. 2008 (47) 2808 - 2812. | DOI: 10.1002/anie.200705415 Request PDF Reprint |
| 35. Diversity–oriented synthesis; a spectrum of approaches and results. read article Richard Spandl, Andreas Bender and David R. Spring | Org. Biomol. Chem. 2008 (6) 1149 - 1158. | DOI: 10.1039/b719372f Request PDF Reprint |
| 34. Integrating high-content screening and ligand-target prediction to identify mechanism of action (Awarded the Thermo Fisher Cellome Award 2009, for the "best published peer-reviewed scientific paper using high-content screening in 2008")  read article download manuscript
Daniel W. Young, Andreas Bender, Jonathan Hoyt, Elizabeth McWhinnie, Gung-Wei Chirn, Charles Y. Tao, John A. Tallarico, Mark Labow, Jeremy L. Jenkins, Timothy J. Mitchison and Yan Feng | Nature Chem. Biol. 2008 (4) 59 - 68 | DOI: 10.1038/nchembio.2007.53 Request PDF Reprint download manuscript |
33. Chemogenomic Data Analysis: Prediction of Small-Molecule Targets and the Advent of Biological Fingerprints read article Andreas Bender, Daniel W. Young, Jeremy L. Jenkins, Martin Serrano, Dmitri Mikhailov, Paul A. Clemons and John W. Davies | Comb. Chem. High-Throughput Screen. 2007 (10) 719 - 731. | DOI: 10.2174/138620707782507313 PDF on GeneGo Website Request PDF Reprint |
32. A Large Descriptor Set and a Probabilistic Kernel-Based Classifier Significantly Improve Druglikeness Classification read article Qingliang Li, Andreas Bender, Jianfeng Pei and Luhua Lai | J. Chem. Inf. Model. 2007 (47) 1776 - 1786. | DOI: 10.1021/ci700107y Request PDF Reprint |
| 31. Understanding False Positives in Reporter Gene Assays: in Silico Chemogenomics Approaches To Prioritize Cell-Based HTS Data Thomas J. Crisman, Christian N. Parker, Jeremy L. Jenkins, Josef Scheiber, Mathis Thoma, Zhao Bin Kang, Richard Kim, Andreas Bender, James H. Nettles, John W. Davies and Meir Glick | J. Chem. Inf. Model 2007 (47) 1319 - 1327. | DOI: 10.1021/ci6005504 Request PDF Reprint |
30. Analysis of Pharmacology Data and the Prediction of Adverse Drug Reactions and Off-Target Effects from Chemical Structure (Cover Picture June 2007 Issue) Andreas Bender, Josef Scheiber, Meir Glick, John W. Davies, Kamal Azzaoui, Jacques Hamon, Laszlo Urban, Steven Whitebread and Jeremy L. Jenkins | ChemMedChem 2007 (2) 861 - 873. | DOI: 10.1002/cmdc.200700026 Request PDF Reprint |
| 29. Modeling Promiscuity Based on in vitro Safety Pharmacology Profiling Data Kamal Azzaoui, Jacques Hamon, Bernard Faller, Steven Whitebread, Edgar Jacoby, Andreas Bender, Jeremy Jenkins and Laszlo Urban | ChemMedChem 2007 (2) 874 - 880. | DOI: 10.1002/cmdc.200700036 Request PDF Reprint |
| 28. Support Vector Inductive Logic Programming Outperforms the Naive Bayes Classifier and Inductive Logic Programming for the Classification of Bioactive Chemical Compounds Edward O. Cannon, Ata Amini, Andreas Bender, Michael J. E. Sternberg, Stephen H. Muggleton, Robert C. Glen and John B. O. Mitchell | J. Comput.-Aided Mol. Des. 2007 (21) 269 - 280. | DOI: 10.1007/s10822-007-9113-3 Request PDF Reprint |
| 27. Flexible 3D Pharmacophores as Descriptors of Dynamic Biological Space James H. Nettles, Jeremy L. Jenkins, Chris Williams, Alex Clark, Andreas Bender, Zhan Deng, John W. Davies, and Meir Glick | J. Mol. Graph. Model. 2007 (26) 622 – 633. | DOI: 10.1016/j.jmgm.2007.02.005 Request PDF Reprint |
| 26. In Silico Target Fishing: Predicting Biological Targets from Chemical Structure Jeremy L. Jenkins, Andreas Bender and John W. Davies | Drug Discov. Today: Technol. 2007 (3) 413 - 421. | DOI: 10.1016/j.ddtec.2006.12.008 Request PDF Reprint |
| 25. "Plate Cherry Picking": A Novel Semi-Sequential Screening Paradigm for Cheaper, Faster, Information-Rich Compound Selection Thomas J. Crisman, Jeremy L. Jenkins, Christian C. Parker, Andreas Bender, Zhan Deng, James H. Nettles, John W. Davies and Meir Glick | J. Biomol. Screen. 2007 (12) 320 - 327. | DOI: 10.1177/1087057107299427 Request PDF Reprint |
| 24. Evolved cellular automata for protein secondary structure prediction imitate the determinants for folding observed in nature Paras Chopra and Andreas Bender | In Silico Biol. 2006 (7) 0007. | Link: www.bioinfo.de/isb/2006/07/0007/ Request PDF Reprint |
| 23. Bridging Chemical and Biological Space: "Target Fishing" Using 2D and 3D Molecular Descriptors James H. Nettles, Jeremy L. Jenkins, Andreas Bender, Zhan Deng, John W. Davies and Meir Glick | J. Med. Chem. 2006 (49) 6802 - 6810. | DOI: 10.1021/jm060902w Request PDF Reprint |
| 22. Chemoinformatics-Based Classification of Prohibited Substances Employed for Doping in Sport Edward O. Cannon, Andreas Bender, David S. Palmer, and John B. O. Mitchell | J. Chem. Inf. Model. 2006 (46) 2369 - 2380. | DOI: 10.1021/ci0601160 Request PDF Reprint |
| 21. "Bayes Affinity Fingerprints" Improve Retrieval Rates in Virtual Screening and Define Orthogonal Bioactivity Space: When Are Multitarget Drugs a Feasible Concept? Andreas Bender, Jeremy L. Jenkins, Meir Glick, Zhan Deng, James H. Nettles, and John W. Davies | J. Chem. Inf. Model 2006 (46) 2445 - 2456. | DOI: 10.1021/ci600197y Request PDF Reprint |
| 20. Melting Point Prediction Employing k-Nearest Neighbor Algorithms and Genetic Parameter Optimization Florian Nigsch, Andreas Bender, Bernd van Buuren, Jos Tissen, Eduard Nigsch, and John B. O. Mitchell | J. Chem. Inf. Model 2006 (46) 2412 - 2422. | DOI: 10.1021/ci060149f Request PDF Reprint |
| 19. Skeletal Diversity Construction via a Divergent Synthetic Strategy. Emma E. Wyatt, Suzanne Fergus, Warren R. J. D. Galloway, Andreas Bender, David J. Fox, Alleyn T. Plowright, Alan S. Jessiman, and David R. Spring | Chem. Commun. 2006 (9) 3296 - 3298. | DOI: 10.1039/b607710b Request PDF Reprint |
| 18. Circular fingerprints: Flexible molecular descriptors with applications from physical chemistry to ADME Robert C. Glen, Andreas Bender, Catrin H Arnby, Lars Carlsson, Scott Boyer, James Smith | IDrugs 2006 (9) 199-204. | BioMedCentral PDF Download BioMedCentral IDrugs Website PubMed Abstract Request PDF Reprint |
| 17. Molecular Similarity: advances in methods, applications and validations in virtual screening and QSAR Andreas Bender, Jeremy L. Jenkins, Qingliang Li, Sam E. Adams, Ed O. Cannon and Robert C. Glen | Annu. Rep. Comput. Chem 2006 (2) 141 - 168. | DOI: 10.1016/S1574-1400(06)02009-3 Request PDF Reprint |
| 16. Analysis of Activity Space by Fragment Fingerprints, 2D Descriptors, and Multitarget Dependent Transformation of 2D Descriptors Alireza Givehchi, Andreas Bender and Robert C. Glen | J. Chem. Inf. Model 2006 (46) 1078 - 1083. | DOI: 10.1021/ci0500233 Request PDF Reprint |
| 15. Harvesting Chemical Information from the Internet Using a Distributed Approach: ChemXtreme M. Karthikeyan, S. Krishnan, Anil Kumar Pandey, and Andreas Bender | J. Chem. Inf. Model. 2006 (46) 452 - 461. | DOI: 10.1021/ci050329+ Request PDF Reprint |
| 14. Characterizing Bitterness: Identification of Key Structural Features and Development of a Classification Model Sarah Rodgers, Robert C. Glen, and Andreas Bender | J. Chem. Inf. Model. 2006 (46) 569 - 576. | DOI: 10.1021/ci0504418 Request PDF Reprint |
| 13. Screening for Dihydrofolate Reductase Inhibitors Using MOLPRINT 2D, a Fast Fragment-Based Method Employing the Naďve Bayesian Classifier: Limitations of the Descriptor and the Importance of Balanced Chemistry in Training and Test Sets Andreas Bender, Hamse Y. Mussa and Robert C. Glen | J. Biomol. Scr. 2005 (10) 658 - 666. | DOI: 10.1177/1087057105281048 Request PDF Reprint |
| 12. Molecular Similarity Searching Using COSMO Screening Charges (COSMO/3PP) Andreas Bender, Andreas Klamt, Karin Wichmann, Michael Thormann and Robert C. Glen | Lect. Notes Comput. Sci 2005 (3695) 175 - 185. | DOI: 10.1007/11560500_16 Request PDF Reprint |
| 11. A Discussion of Measures of Enrichment in Virtual Screening: Comparing the Information Content of Descriptors with Increasing Levels of Sophistication Andreas Bender and Robert C. Glen | J. Chem. Inf. Model. 2005 (45) 1369 - 1375. | DOI: 10.1021/ci0500177 Request PDF Reprint |
| 10. General Melting Point Prediction Based on a Diverse Compound Data Set and Artificial Neural Networks M. Karthikeyan, Robert C. Glen and Andreas Bender | J. Chem. Inf. Model. 2005 (45) 581 - 590. | DOI: 10.1021/ci0500132 Request PDF Reprint |
| 9. Encoding and Decoding Graphical Chemical Structures as Two-Dimensional (PDF417) Barcodes M. Karthikeyan and Andreas Bender | J. Chem. Inf. Model. 2005 (45) 572 - 580. | DOI: 10.1021/ci049758i Request PDF Reprint |
| 8. Assessment of structural diversity in combinatorial synthesis Suzanne Fergus, Andreas Bender and David R. Spring | Curr. Op. Chem.Biol. 2005 (9) 304 - 309. | DOI: 10.1016/j.cbpa.2005.03.004 Request PDF Reprint |
| 7. Diversity Oriented Synthesis: A Challenge for Synthetic Chemists Andreas Bender, Suzanne Fergus, Warren R. J. D. Galloway, Freija G. Glansdorp, David M. Marsden, Rebecca L. Nicholson, Richard J. Spandl, Gemma L. Thomas, Emma E. Wyatt, Robert C. Glen and David R. Spring | In Ernst Schering Res. Found. Workshop 2005 (58), Chemical Genomics - Small Molecule Probes to Study Cellular Function | Download PDF (Manuscript, PDF, 500kB) |
| 6. Molecular similarity: a key technique in molecular informatics Andreas Bender and Robert C. Glen | Org. Biomol. Chem. 2004 (2) 3204 - 3218. | DOI: 10.1039/b409813g Download PDF(1.3MB) The "Green Policy" of the RSC allows authors to put PDF articles on their personal websites. See further information here. |
| 5.Molecular surface point environments for virtual screening and the elucidation of binding patterns (MOLPRINT 3D) Andreas Bender, Hamse Y. Mussa, Gurprem S. Gill and Robert C. Glen | J. Med. Chem. 2004 (47) 6569-6583. | DOI: 10.1021/jm049611i Request PDF Reprint |
| 4. Molecular surface point environments for virtual screening and the elucidation of binding patterns (MOLPRINT). Andreas Bender, Hamse Y. Mussa, Gurprem S. Gill and Robert C. Glen | IEEE Int. Conf. Syst. Man Cybern., 2004 (5) 4553 - 4558. | LinkOut (IEEExplore): IEEExplore Download PDF |
| 3. Similarity searching of chemical databases using atom environment descriptors: evaluation of performance (MOLPRINT 2D). Andreas Bender, Hamse Y. Mussa, Robert C. Glen and Stephan Reiling | J. Chem. Inf. Comput. Sci. 2004 (44) 1708 - 1718. | DOI: 10.1021/ci0498719 Request PDF Reprint |
| 2. Molecular Similarity Searching using Atom Environments, Information-Based Feature Selection and a Naďve Bayesian Classifier Andreas Bender, Hamse Y. Mussa, Robert C. Glen and Stephan Reiling | J. Chem. Inf. Comput. Sci. 2004 (44) 170 - 178. | DOI: 10.1021/ci034207y Request PDF Reprint |
| 1. Properties and prediction of mitochondrial transit peptides from Plasmodium
falciparum Andreas Bender, Giel van Dooren, Stuart Ralph, Geoffrey I. McFadden and Gisbert Schneider | Mol. Biochem. Parasitol. 2003 (132) 59 - 66. | DOI: 10.1016/j.molbiopara.2003.07.001 Request PDF Reprint |
| Other Publications | Event / Reference | Reference | Link |
| "Molecular Similarity" | Chapter for Interactive Drug Design Course "Molecular Conceptor" | (new chapter in version 2.5, released January 2006) | www.molecular-conceptor.com |
| Cutting Edge Approaches to Drug Design (Conference Report) | London, 19 March 2003 | Biosilico, 2003(1), 53-54 | read (PDF) |
In the following table some presentations are linked as downloadable PPT/PDF files, some are not. Usually there is a reason - please e-mail me and I can see what I can do.
| Oral Presentations | Title | Event | Link |
| Andreas Bender | Merging High-Content Screening and in silico Approaches for Compound Profiling and Mode-of-Action Analysis | Bio-IT World Expo 2008, Boston/MA, April 2008 | n/a |
| Andreas Bender | In Silico Drug Design: Identification of Active Compounds and the Prediction of On-Target and Off- Target Effects | 6th Annual Congress: G Protein-Coupled Receptors in Drug Discovery, Berlin, March 2008 | n/a |
| Andreas Bender | Compound Profiling by Predicting On-Target Activities, Compound Promiscuity and Adverse Drug Reactions | 3rd CHI Conference on Compound Profiling, Philadelphia/PA, October 2007 | n/a |
| Andreas Bender | Target-Prediction for Small Molecules – Know More About On-Target and Off- Target Effects of Your Compounds | MedChem 2007, Boston, September 2007 | n/a |
| Andreas Bender, Jeremy L. Jenkins, John W. Davies | "Phylochemical Tree" for drug targets: Putting biological activities into context via ligand-based similarity measures. | 234th ACS National Meeting, Boston/MA, August 2007. | n/a |
| Andreas Bender | In Silico Drug Design: From Virtual Screening and the Prediction of Adverse Drug Reactions to the Shape of Chemical Space | International Conference on Chemoinformatics, Pune, January 2007 | n/a |
| Andreas Bender | In Silico Drug Design: Identification of Active Compounds and the Prediction of On-Target and Off-Target Effects | MedChem USA 2006, San Diego, September 2006 | n/a |
| Andreas Bender | Molecular Similarity - Approaches, Advances and Illusions | EuroQSAR 2006, Mediterrenean Sea, September 2006 | n/a |
| Andreas Bender, Robert C. Glen | Molecular Similarity - Approaches, Advances and Illusions | UK QSAR Meeting, Organon, Scotland - October 2005 | PPT Slides |
| Andreas Bender, Robert C. Glen | Novel Approaches To Molecular Similarity (‘Molecular Similarity Searching Using COSMO Screening Charges’) | CompLife, Konstanz, Germany - September 2005 | PPT Slides |
| Andreas Bender | Similarity Searching Based on COSMO Screening Charges (And Some Findings On Current Descriptors) | International Conference on Chemical Structures, Noordwijkerhout, The Netherlands - June 2005 | PPT Slides |
| Andreas Bender | Novel Approaches To Molecular Similarity | JCF Fruehjahrssymposium, Berlin, Germany - 8 April 2005 | PPT Slides |
| Andreas Bender, Hamse Y. Mussa, Robert C. Glen | Similarity Searching Employing Surface Fingerprints - Using Spatial Data for Meaningful Feature Selection | Recent Advances of Chemical Technologies in Pharmaceutical Industry, London, UK - 24 November 2004 | PPT Slides |
| Andreas Bender, Hamse Y. Mussa, Robert C. Glen | Virtual Screening Using Atom Environments and Surface Point Environments (MOLPRINT) - Evaluation of Complementary 2D and 3D Methods | eCheminfo 2004 (web-based conference), 8-19 November 2004 | PPT Slides |
| Andreas Bender, Hamse Y. Mussa, Gurprem S. Gill, Robert C. Glen | Similarity Searching Employing Surface Fingerprints - Using Spatial Data for Meaningful Feature Selection | Third Joint Sheffield Conference on Chemoinformatics, Sheffield, UK - 21 April 2004 | PPT Slides |
| Andreas Bender, Hamse Y. Mussa, Stephan Reiling, Robert C. Glen | Similarity searching using Atom Environments, information gain based feature selection and the Naďve Bayesian Classifier | American Chemical Society Meeting, Anaheim, USA - 29 March 2004 | PPT Slides |
| Andreas Bender, Hamse Y. Mussa, Stephan Reiling, Robert C. Glen | Molecular Similarity Searching Using Atom Environments | Pfizer Graduate Symposium, Cambridge, UK - 20 October 2003 | - |
| Andreas Bender, Hamse Y. Mussa, Stephan Reiling, Robert C. Glen | Molecular Similarity Searching Using Atom Environments | Daylight EuroMUG 2003, Cambridge, UK - 10 October 2003 | PPT Slides |
| Theses / Research Projects | Project Type | Link |
| New Approaches To Molecular Similarity. | PhD Thesis, University of Cambridge, Cambridge, UK, 2005 | read (2.9 MB PDF) |
| New Approaches to Molecular Similarty | CPGS (1st year PhD) Thesis (Cambridge University) | read (PDF) |
| Merkmalsextraktion mitochondrialer Targetingsequenzen in Plasmodium falciparum | Master Thesis (German, University of Frankfurt) | read (PDF) |
| Structure Modeling Of Aluminosilsesquioxanes | BS Project (Trinity College Dublin) | read (PDF) |
| Chemistry of Aluminosiloxanes | BS Project (Trinity College Dublin) | read (PDF) |
| Poster Presentations / Conference Proceedings | Title | Event, Date and Place | Link |
| Uli Fechner and Andreas Bender | BayCATS - Combining the Potency of a Pharmacophore Descriptor With the Power of the Bayes Classifier | MGMS 2005, Dublin, September 2005 | PPT File |
| Fiona T. Mc Cahey, Philip M. Marsden, Andreas Bender, Jos W. M. Tissen, Werner Klaffke and Robert C. Glen | Molecular Similarity as a guide to Safety Pharmacology | MGMS 2005, Dublin, September 2005 | PPT File |
| Andreas Bender, Stephan Reiling, Hamse Y. Mussa, Robert C. Glen | Novel Molecular Similarity Searching Using Atom Environments, Information-Based Feature Selection and a Naďve Bayesian Classifier | 23rd SGAI International Conference on Innovative Techniques and Applications of Artificial Intelligence 2003, 15-17 December 2003, Peterhouse College, Cambridge | PPT File |
| Andreas Bender, Stephan Reiling, Hamse Y. Mussa, Robert C. Glen | Novel Molecular Similarity Searching Using Atom Environments, Information-Based Feature Selection and a Naďve Bayesian Classifier | eCheminformatics 2003, 10 - 14 November 2003 (Web-Based Conference) | PPT File |
| Andreas Bender, Stephan Reiling, Hamse Y. Mussa, Robert C. Glen | Molecular Similarity Searching using Atom Environments, Information-Based Feature Selection and a Naďve Bayesian Classifier | German Chemical Society Annual Meeting, 7 - 9 October 2003, Munich | PPT File |
| Andreas Bender, Stephan Reiling, Hamse Y. Mussa, Robert C. Glen | Molecular Similarity Searching using Atom Environments, Information-Based Feature Selection and a Naďve Bayesian Classifier | RSC/SOCI Medicinal Chemistry Symposium, 8 September 2003, Cambridge | PPT File |
| Non-scientific Articles | Journal | Link |
| Cheminformatics: Your Personal Ticket Into the Thriving Biotech World? | Science's NextWave | read(HTML) |
| Networking Is the Golden Key | Science's NextWave | read (HTML) |