` Andreas Bender
The review on molecular similarity can be downloaded free of charge here.

Edited Books
Computational Approaches in Cheminformatics and BioinformaticsRajarshi Guha and Andreas Bender (Eds.), Wiley-Blackwell, 2012
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Handbook of Chemoinformatics AlgorithmsJean-Loup Faulon and Andreas Bender (Eds.), Chapman & Hall, 2010
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Scientific ArticlesReferenceLink
126. Polypharmacology modelling using proteochemometrics (PCM): recent methodological developments, applications to target families, and future prospects.


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Isidro Cortes-Ciriano, Qurrat Ul Ain, Vigneshwari Subramanian, Eelke B. Lenselink, Oscar Mendez-Lucio, Adriaan P. IJzerman, Gerd Wohlfahrt, Peteris Prusis, Therese E. Malliavin, Gerard J. P. van Westen, and Andreas Bender.
MedChemComm. 2015 (in press).DOI: 10.1039/C4MD00216D

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125. Connecting gene expression data from connectivity map and in silico target predictions for small molecule mechanism-of-action analysis.


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Aakash Chavan Ravindranath, Nolen Perualila-Tan, Adetayo Kasim, Georgios Drakakis, Sonia Liggi, Suzanne C. Brewerton, Daniel Mason, Michael J. Bodkin, David A. Evans, Aditya Bhagwat, Willem Talloen, Hinrich W. H. Göhlmann, QSTAR Consortium, Ziv Shkedy, and Andreas Bender.
Mol. Biosyst. 2015 (11) 86 - 96 .DOI: 10.1039/C4MB00328D

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124. A community computational challenge to predict the activity of pairs of compounds.


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Mukesh Bansal, Jichen Yang, Charles Karan, Michael P. Menden, James C. Costello, Hao Tang, Guanghua Xiao, et al.
Nature Biotechnol.2014 (32) 1213 - 1222.DOI: 10.1038/nbt.3052

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123. Synthesis and Characterization of Novel 2-Amino-Chromene-Nitriles that Target Bcl-2 in Acute Myeloid Leukemia Cell Line.


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Hosadurga K. Keerthy, Manoj Garg, Chakrabhavi D. Mohan, Vikas Madan, Deepika Kanojia, Rangappa Shobith, Shivananju Nanjundaswamy, Daniel J. Mason, Andreas Bender, Basappa, Kanchugarakoppal S. Rangappa, and H. Phillip Koeffler
PLoS ONE 2014 (9) e107118.DOI: 10.1371/journal.pone.0107118

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122. 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.


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Chakrabhavi Dhananjaya Mohan, Hanumantharayappa Bharathkumar, Krishna C. Bulusu, Vijay Pandey, Shobith Rangappa, Julian E. Fuchs, Muthu K. Shanmugam, Xiaoyun Dai, Feng Li, Amudha Deivasigamani, Kam M. Hui, Alan Prem Kumar, Peter E. Lobie, Andreas Bender, Basappa, Gautam Sethi, and Kanchugarakoppal S. Rangappa
J. Biol. Chem. 2014 (289) 34296 - 34307.DOI: 10.1074/jbc.M114.601104

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121. Novel Synthetic Biscoumarins Target Tumor Necrosis Factor-α in Hepatocellular Carcinoma in Vitro and in Vivo.


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Hosadurga Kumar Keerthy, Chakrabhavi Dhananjaya Mohan, Kodappully Sivaraman Siveen, Julian E. Fuchs, Shobith Rangappa, Mahalingam S. Sundaram, Feng Li, Kesturu S. Girish, Gautam Sethi, Basappa, Andreas Bender, and Kanchugarakoppal Subbegowda Rangappa.
J. Biol. Chem. 2014 (289) 31879 - 31890.DOI: 10.1074/jbc.M114.593855

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120. Modelling ligand selectivity of serine proteases using integrative proteochemometric approaches improves model performance and allows the multi-target dependent interpretation of features.


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Qurrat U. Ain, Oscar Mendez-Lucio, Isidro Cortés Ciriano, Therese Malliavin, Gerard J. P. van Westen, and Andreas Bender
Integr. Biol. 2014 (6) 1023 - 1033 .DOI: 10.1039/C4IB00175C

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119. Synthesis, biological evaluation and in silico and in vitro mode-of-action analysis of novel dihydropyrimidones targeting PPAR-γ.


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Hanumantharayappa Bharathkumar, Shardul Paricharak, K. R. Dinesh, Kodappully Sivaraman Siveen, Julian E. Fuchs, Shobith Rangappa, C. D. Mohan, Nima Mohandas, Alan Prem Kumar, Gautam Sethi, Andreas Bender, Basappa, and K. S. Rangappa.
RSC Advances 2014 (4) 45143 - 45146.DOI: 10.1039/C4RA08713E

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118. Novel Benzoxazine-Based Aglycones Block Glucose Uptake In Vivo by Inhibiting Glycosidases.


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Hanumantharayappa Bharathkumar, Mahalingam S. Sundaram, Swamy Jagadish, Shardul Paricharak, Mahadevappa Hemshekhar, Daniel Mason, Kempaiah Kemparaju, Kesturu S. Girish, Basappa, Andreas Bender, and Kanchugarakoppal S. Rangappa.
PLoS ONE 2014 (9) e102759.DOI: 10.1371/journal.pone.0102759

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117. Proteochemometric modeling in a Bayesian framework.


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Isidro Cortes-Ciriano, Gerard J. P. van Westen, Eelke Bart Lenselink, Daniel S. Murrell, Andreas Bender, and Therese Malliavin.
J. Cheminf. 2014 (6) 35.DOI: 10.1186/1758-2946-6-35

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116. A community effort to assess and improve drug sensitivity prediction algorithms.


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James C. Costello, Laura M. Heiser, Elisabeth Georgii, Mehmet Gönen, Michael P. Menden, et al.
Nature Biotechnol. 2014 (32) 1202 - 1212.DOI: 10.1038/nbt.2877

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115. Towards predictive resistance models for agrochemicals by combining chemical and protein similarity via proteochemometric modelling.


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Gerard J. P. van Westen, Andreas Bender and John P. Overington.
J. Chem. Biol 2014 (7) 119 - 123.DOI: 10.1007/s12154-014-0112-2

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114. Comparative mode-of-action analysis following manual and automated phenotype detection in Xenopus laevis.


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Georgios Drakakis, Adam E. Hendry, Kimberley Hanson, Suzanne C. Brewerton, Michael J. Bodkin, David A. Evans, Grant N. Wheeler, and Andreas Bender.
MedChemComm 2014 (5) 386 - 296.DOI: 10.1039/C3MD00313B

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113. Biofragments: an approach towards predicting protein function using biologically-related fragments, and its application to Mycobacterium tuberculosis CYP126.


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Sean A. Hudson, Ellene H. Mashalidis, Andreas Bender, Kirsty J. McLean, Andrew W. Munro and Chris Abell.
ChemBioChem 2014 (15) 549 - 555.DOI: 10.1002/cbic.201300697

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112. How Diverse Are Diversity Assessment Methods? A Comparative Analysis and Benchmarking of Molecular Descriptor Space.


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Alexios Koutsoukas, Shardul Paricharak, Warren R. J. D. Galloway, David R. Spring, Adriaan P. IJzerman, Robert C. Glen, David Marcus and Andreas Bender.
J. Chem. Inf. Model. 2014 (54) 230 - 242.DOI: 10.1021/ci400469u

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111. Synthesis and biological evaluation of tetrahydropyridinepyrazoles ('PFPs') as inhibitors of STAT3 phosphorylation.


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Revanna C. N., Basappa, Srinivasa V, Feng Li, Kodappully Sivaraman Siveen, Xiaoyun Dai, Shivananju Nanjunda Swamy, Bhadregowda D. G, Gautam Sethi, Mantelingu K., Andreas Bender and Rangappa K.S.
MedChemComm 2014 (5) 32 - 40.DOI: 10.1039/C3MD00119A

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110. Predicting Toxic Effects of Metabolites.


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Andreas Bender.
In: Drug Metabolism Prediction. Johannes Kirchmair (Ed.), Wiley, New York 2014.DOI: http://eu.wiley.com/WileyCDA/WileyTitle/productCd-3527335668.html

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109. 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.


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Shardul Paricharak, Tom Klenka, Martin Augustin, Umesh A Patel and Andreas Bender.
J. Cheminf. 2013 (5) 49.DOI: http://dx.doi.org/10.1186/1758-2946-5-49

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108. Evaluation of antioxidant and antimicrobial activities of the phenolic composition of Algerian Arbutus unedo L. Roots.


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Nassim Djabou, Mohamed El Amine Dib, Hocine Allali, Andreas Bender, Mohammad A. Kamal, Said Ghalem and Boufeldja Tabti.
Pharmacognosy J. 2013 (5) 275 - 280.DOI: 10.1016/j.phcgj.2013.09.003

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107. Experimental Confirmation of New Drug-Target Interactions Predicted by Drug Profile Matching.


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Laszlo Vegner, Agnes Peragovics, Laszlo Tombor, Balazs Jelinek, Pal Czobor, Andreas Bender, Zoltan Simon and Andras Malnasi-Csizmadia
J. Med. Chem. 2013 (56) 8377 - 8388.DOI: 10.1021/jm400813y

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106. Design, Synthesis, and Biological Evaluation of an Allosteric Inhibitor of HSET that Targets Cancer Cells with Supernumerary Centrosomes.


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Ciorsdaidh A. Watts, Frances M. Richards, Andreas Bender, Peter J. Bond, Oliver Korb, Oliver Kern, Michelle Riddick, Paul Owen, Rebecca M. Myers, Fanni Gergely, Jordan Raff, Duncan I. Jodrell and Steven V Ley.
Chem. Biol. 2013 (20) 1399 - 1410.DOI: 10.1016/j.chembiol.2013.09.012

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105. Benchmarking of protein descriptor sets in proteochemometric modeling (part 2): modeling performance of 13 amino acid descriptor sets.


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Gerard J. P. van Westen, Remco F. Swier, Isidro Cortes-Ciriano, Jörg K. Wegner, John P. Overington, Adriaan P. IJzerman, Herman W. T. van Vlijmen and Andreas Bender
J. Cheminf. 2013 (5) 42.DOI: 10.1186/1758-2946-5-42

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104. Benchmarking of protein descriptor sets in proteochemometric modeling (part 1): comparative study of 13 amino acid descriptor sets.


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Gerard J. P. van Westen, Remco F. Swier, Jörg K. Wegner, Adriaan P. IJzerman, Herman W. T. van Vlijmen and Andreas Bender
J. Cheminf. 2013 (5) 41.DOI: 10.1186/1758-2946-5-41

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103. Extensions to In Silico Bioactivity Predictions Using Pathway Annotations and Differential Pharmacology Analysis: Application to Xenopus laevis Phenotypic Readouts.


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Sonia Liggi, Georgios Drakakis, Adam Hendry, Kimberley M. Hanson, Suzanne C. Brewerton, Grant N. Wheeler, Michael J. Bodkin, David A. Evans and Andreas Bender
Mol. Inf. 2013 (11-12) 1009 - 1024.DOI: 10.1002/minf.201300102

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102. In silico target predictions: defining a benchmarking dataset and comparison of performance of the multiclass Naïve Bayes and Parzen-Rosenblatt Window.


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Alexios Koutsoukas, Robert Lowe, Yasaman KalantarMotamedi, Hamse Y. Mussa, Werner Klaffke, John B. O. Mitchell, Robert C. Glen and Andreas Bender
J. Chem. Inf. Model. 2013 (53) 1957 - 1966.DOI: 10.1021/ci300435j

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101. Linking Ayurveda and Western Medicine by Integrative Analysis.


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Fazlin Mohd Fauzi, Alexios Koutsoukas, Robert Lowe, Kalpana Joshi, Tai-Ping Fan, Robert C. Glen and Andreas Bender
J. Ayurveda Integr. Med. 2013 (4) 117 - 119.DOI: 10.1371/10.4103/0975-9476.113882

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100. Diversity selection of compounds based on 'Protein Affinity Fingerprints' improves sampling of bioactive chemical space.


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Ha P. Nguyen, Alexios Koutsoukas, Fazlin Mohd Fauzi, Georgios Drakakis, Mateusz Maciejewski, Robert C. Glen and Andreas Bender
Chem. Biol. Drug Des. 2013 (82) 252 - 266.DOI: 10.1111/cbdd.12155

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99. Computer-Aided ('In silico') Approaches in the Mode-of-Action Analysis and Safety Assessment of Ostarine and 4-Methylamphetamine.


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Fazlin Mohd Fauzi, Alexios Koutsoukas, Andrew Cunningham, Ana Gallegos, Roumen Sedefov and Andreas Bender
Human Psychopharmacol. 2013 (28) 365 - 378.DOI: 10.1002/hup.2322

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98. Significantly Improved HIV Inhibitor Efficacy Prediction Employing Proteochemometric Models Generated From Antivirogram Data.


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Gerard J.P. van Westen, Alwin Hendriks, Jörg K. Wegner, Adriaan P. IJzerman, Herman W.T. van Vlijmen and Andreas Bender
PLoS Comp. Biol. 2013 (9) e1002899.DOI: 10.1371/journal.pcbi.1002899

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97. Chemogenomics Approaches to Rationalizing the Mode-of-Action of Traditional Chinese and Ayurvedic Medicines.


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Fazlin Mohd Fauzi, Alexios Koutsoukas, Rob Lowe, Kalpana Joshi, Tai-Ping Fan, Robert C. Glen and Andreas Bender
J. Chem. Inf. Model. 2013 (53) 661 - 673.DOI: 10.1021/ci3005513

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96. Experimental Validation of In Silico Target Predictions on Synergistic Protein Targets.


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Isidro Cortes-Ciriano, Alexios Koutsoukas, Olga Abian, Robert C. Glen, Adrian Velazquez-Campoy and Andreas Bender
MedChemComm 2013 (4) 278 - 288.DOI: 10.1039/C2MD20286G

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95. Identifying Novel Adenosine Receptor Ligands by Simultaneous Proteochemometric Modeling of Rat and Human Bioactivity Data.


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Gerard J. P. van Westen, Olaf O. van den Hoven, Rianne van der Pijl, Thea Mulder-Krieger, Henk de Vries, Jorg K. Wegner, Adriaan P. IJzerman, Herman W. T. van Vlijmen and Andreas Bender
J. Med. Chem 2012 (55) 7010 - 7020.DOI: 10.1021/jm3003069

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94. A Two-Directional Strategy for the Diversity-Oriented Synthesis of Macrocyclic Scaffolds.


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Kieron O'Connell, Henning Beckmann, Luca Laraia, Helen Horsley, Andreas Bender, Ashok Venkitaraman and David Spring.
Org. Biomol. Chem. 2012 (10) 7454 - 7551.DOI: 10.1039/C2OB26272J

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93. Using multiobjective optimization and energy minimization to design an isoform-selective ligand of the 14-3-3 protein.


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Hernando Sanchez-Faddeev, Michael T. M. Emmerich, Fons J. Verbeek, Andrew H. Henry, Simon Grimshaw, Herman P. Spaink, Herman W. van Vlijmen and Andreas Bender
Lect. Notes Comput. Sci. 2012 (7610) 12 - 24.DOI: 10.1007/978-3-642-34032-1_3

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92. Multi-Objective Evolutionary Design of Adenosine Receptor Ligands.


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Eelke van der Horst, Patricia Marques-Gallego, Thea Mulder-Krieger, Jacobus van Veldhoven, Johannes Kruisselbrink, Alexander Aleman, Michael T. M. Emmerich, Johannes Brussee, Andreas Bender and Adriaan P. IJzerman
J. Chem. Inf. Model. 2012 (52) 1713 - 1721.DOI: 10.1021/ci2005115

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91. Predicting Genes Involved in Human Cancer Using Network Contextual Information.


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Hossein Rahmani, Hendrik Blockeel and Andreas Bender
J. Integr. Bioinf. 2012 (9) 210.DOI: 10.2390/biecoll-jib-2012-210

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90. A Prospective Cross-Screening Study on G Protein-Coupled Receptors: Lessons Learned in Virtual Compound Library Design.


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Marijn P. A. Sanders, Luc Roumen, Eelke van der Horst, J. Robert Lane, Henry F. Vischer,Jody van Offenbeek, Henk de Vries, Stefan Verhoeven, Ken Y. Chow, Folkert Verkaar, Margot W. Beukers, Ross McGuire, Rob Leurs, Adriaan P. IJzerman, Jacob de Vlieg, Iwan J. P. de Esch, Guido J.R. Zaman, Jan P. G. Klomp, Andreas Bender and Chris de Graaf.
J. Med. Chem 2012 (55) 5311 - 5325.DOI: 10.1021/jm300280e

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89. Cheminformatics.


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Joerg K. Wegner, Rajarshi Guha, Aaron Sterling, Andreas Bender, Jean-Loup Faulon, Janna Hastings, Noel O’Boyle, John Overington, Herman Van Vlijmen and Egon Willighagen.
Commm. ACM 2012 (55) 65 - 75..DOI: 10.1145/2366316.2366334

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88. Recognizing Pitfalls in Virtual Screening: A Critical Review.


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Thomas Scior, Gary Tresadern, Andreas Bender, Jose Luis Medina-Franco, Karina Martinez-Mayorga, Thierry Langer, Karina Cuanalo-Contreras and Dimitris K Agrafiotis.
J. Chem. Inf. Model. 2012 (52) 867 - 881.DOI: 10.1021/ci200528d

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87. A-Ring Dihalogenation Increases the Cellular Activity of Combretastatin-Templated Tetrazoles.


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Thomas M. Beale, Daniel M. Allwood, Andreas Bender, Peter J. Bond, James D. Brenton, D. Stephen Charnock-Jones, Steven V. Ley, Rebecca M. Myers, James W. Shearman, Jill Temple, Jessica Unger, Ciorsdaidh A. Watts and Jian Xian.
ACS Med. Chem. Lett. 2012 (3) 177 - 181.DOI: 10.1021/ml200149g

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86. Computational Prediction of Metabolism: Sites, Products, SAR, P450 Enzyme Dynamics, and Mechanisms.


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Johannes Kirchmair, Mark J. Williamson, Jonathan D. Tyzack, Lu Tan, Peter J. Bond, Andreas Bender and Robert C. Glen.
J. Chem. Inf. Model 2012 (52) 617 - 648.DOI: 10.1021/ci200542m

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85. The challenges involved in Modeling Toxicity Data in silico: A Review.


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M.Paul Gleeson, Sandeep Modi, Andreas Bender, Richard L. Marchese Robinson, Johannes Kirchmair, Malinee Promkatkaew, Supa Hannongbua and Robert C. Glen.
Curr. Pharm. Des. 2012 (18) 1266 - 1291.DOI: http://www.ingentaconnect.com/content/ ben/cpd/2012/00000018/00000009/art00008

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84. Bridging Chemical and Biological Data: Implications for Pharmaceutical Drug Discovery.


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Jeremy L. Jenkins, Josef Scheiber, Dmitri Mikhailov, Andreas Bender, Ansgar Schuffenhauer, Ben Cornett, Vivien Chan, Jason Kondracki, Bernhard Rohde, and John W. Davies.
In: Computational Approaches in Cheminformatics and Bioinformatics, Wiley, Rajarshi Guha and Andreas Bender (Eds.) 2011DOI: http://eu.wiley.com/WileyCDA/WileyTitle/productCd-0470384417.html

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83. Understanding and Classifying Metabolite Space and Metabolite-Likeness.


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Julio E. Peironcely, Theo Reijmers, Leon Coulier, Andreas Bender and Thomas Hankemeier.
PLoS One 2011 e28966.DOI: 10.1371/journal.pone.0028966

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82. Which Compound to Select in Lead Optimization? Prospectively Validated Proteochemometric Models Guide Preclinical Development.


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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

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81. Substructure-Based Virtual Screening for Adenosine A2A Receptor Ligands.


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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

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80. Collaboration-based Function Prediction in Protein-Protein Interaction Networks.


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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

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79. Interaction-Based Feature Selection for Predicting Cancer-Related Proteins in Protein-Protein Interaction Networks.


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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

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78. From in silico target prediction to multi-target drug design: Current databases, methods and applications.


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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

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77. Online Chemical Modeling Environment (OCHEM): Web Platform for Data Storage, Model Development and Publishing of Chemical Information.


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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

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76. P-glycoprotein Substrate Models Using Support Vector Machines Based on a Comprehensive Dataset.


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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

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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

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74. Diversity-oriented synthesis of macrocyclic peptidomimetics.


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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

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73. Increased Diversity of Libraries from Libraries: Chemoinformatic Analysis of Bis-Diazacyclic Libraries.


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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

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72. Chemogenomics Approaches for Receptor Deorphanization and Extensions of the Chemogenomics Concept to Phenotypic Space.


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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

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71. Proteochemometric modeling as a tool to design selective compounds and for extrapolating to novel targets.


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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

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70. Bayesian Methods in Virtual Screening and Chemical Biology.


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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

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69. How similar are those molecules after all? Use two descriptors and you will have three different answers.


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Andreas Bender.
Exp. Op. Drug Discov. 2010 (5) 1141 - 1151.DOI: 10.1517/17460441.2010.517832

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68. Virtual Activity Profiling of Bioactive Molecules by 1D Fingerprinting.


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Aimy Sebastian, Andreas Bender and Vibin Ramakrishnan.
Mol. Inf. 2010 (29) 773 - 779.DOI: 10.1002/minf.201000075

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67. Collaboration-based Function Prediction in Protein-Protein Interaction networks.


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Hossein Rahmani, Hendrik Blockeel and Andreas Bender.
In: Proc. 4th Int. Workshop in Machine Learn. Syst. Biol. (MLSB10) 2010 55 - 58.DOI: N/A

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66. A novel chemogenomics analysis of G protein coupled receptors (GPCRs) and their ligands: a potential strategy for receptor de-orphanization.


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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

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65. Dynamic clustering threshold reduces conformer ensemble size while maintaining a biologically relevant ensemble.


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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

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64. Prospective Validation of a Comprehensive In silico hERG model and its Applications to Commercial Compound and Drug Databases.


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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

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63. Mining protein dynamics from sets of crystal structures using "consensus structures".


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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

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62. Predicting the functions of proteins in Protein-Protein Interaction networks from global information.


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Hossein Rahmani, Hendrik Blockeel and Andreas Bender.
J. Mach. Learn. Res. 2010 (8) 82 - 97.DOI: Journal Article

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61. Alpha Shapes Applied to Molecular Shape Characterization Exhibit Novel Properties Compared to Established Shape Descriptors.


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J. Anthony Wilson, Andreas Bender, Taner Kaya and Paul A. Clemons.
J. Chem. Inf. Model. 2009 (49) 2231 - 2241.DOI: 10.1021/ci900190z

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60. Scaffold Diversity Analysis of Compound Data Sets Using an Entropy-Based Measure.


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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

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59. Predicting the functions of proteins in PPI networks from global information.


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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

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58. Multi-parameter Phenotypic Profiling: Characterization of Small-molecule Compounds Based on Their Effects on Cells.


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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

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57. Mapping Adverse Drug Reactions in Chemical Space.


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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

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56. Knowledge-based and computational approaches based on in vitro safety pharmacology.


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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

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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.


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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

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53. Plate-Based Diversity Selection Based on Empirical HTS Data to Enhance the Number of Hits and Their Chemical Diversity.


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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

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52. The discovery of antibacterial agents using diversity-oriented synthesis.


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Warren R. J. D. Galloway, Andreas Bender, Martin Welch and David R. Spring
Chem. Commun. 2009, 2446 - 2462.DOI: 10.1039/b816852k

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51. Fishing the target of Antitubercular Compounds: In silico target deconvolution model development and validation.


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Philip Prathipati, Ngai Ma, Ujjini Manjunatha and Andreas Bender.
J. Proteome Res. 2009 (8) 2788 - 2798 DOI: 10.1021/pr8010843

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50. Use of Ligand Based Models for Protein Domains To Predict Novel Molecular Targets and Applications To Triage Affinity Chromatography Data


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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

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49. SPREAD – Exploiting chemical features that cause differential activity behaviour.


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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

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48. Combining Aggregation with Pareto Optimization: A Case Study in Evolutionary Molecular Design.


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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

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47. How Similar Are Similarity Searching Methods? A Principal Component Analysis of Molecular Descriptor Space


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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

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46. A Comprehensive Systems Chemical Biology Analysis Gains Insight into Off-Target Mediated Effects of Drug Candidates


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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

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45. Characterization of Activity Landscapes Using 2D and 3D Similarity Methods: Consensus Activity Cliffs


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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

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44. Substructure Mining of GPCR Ligands Reveals Activity-Class Specific Functional Groups in an Unbiased Manner


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Eelke van der Horst, Yasushi Okuno, Andreas Bender, and Adriaan P. IJzerman.
J. Chem. Inf. Model 2009 (49) 348 - 360.DOI: 10.1021/ci8003896

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43. Computational Methods to Support High-Content Screening: From Compound Selection and Data Analysis to Postulating Target Hypotheses


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Anne Kümmel, Daniela Gabriel, Christian N. Parker and Andreas Bender.
Exp. Op. Drug Discov. 2009 (4) 5 - 13.DOI: 10.1517/17460440802586434

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42. A Scenario Implementation in R for SubtypeDiscovery Examplified on Chemoinformatics Data


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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

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41. Ligand-Target Prediction Using Winnow and Naive Bayesian Algorithms and the Implications of Overall Performance Statistics


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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

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40. A Quantitative bgl Operon Model for E. coli Requires BglF Conformational Change for Sugar Transport


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Paras Chopra and Andreas Bender
Trans. on Comput. Syst. Biol. 2008 (9) 1-22.DOI: to be assigned

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39. Which aspects of HTS are empirically correlated with downstream success?


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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

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38. Distributed Chemical Computing Using ChemStar: An Open Source Java RMI Architecture applied to Large Scale Molecular Data from PubChem


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M. Karthikeyan, Anil Kumar Pandey, S. Krishnan, Andreas Bender and Alexander Tropsha.
J. Chem. Inf. Model. 2008 (48) 691 - 703.DOI: 10.1021/ci700334f

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37. "Virtual Fragment Linking": An Approach To Identify Potent Binders from Low Affinity Fragment Hits


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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

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36. Anti-MRSA Agent Discovery Using Diversity-Oriented Synthesis


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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

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35. Diversity–oriented synthesis; a spectrum of approaches and results.


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Richard Spandl, Andreas Bender and David R. Spring
Org. Biomol. Chem. 2008 (6) 1149 - 1158.DOI: 10.1039/b719372f

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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")


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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 - 68DOI: 10.1038/nchembio.2007.53

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download manuscript
33. Chemogenomic Data Analysis: Prediction of Small-Molecule Targets and the Advent of Biological Fingerprints


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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

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32. A Large Descriptor Set and a Probabilistic Kernel-Based Classifier Significantly Improve Druglikeness Classification


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Qingliang Li, Andreas Bender, Jianfeng Pei and Luhua Lai
J. Chem. Inf. Model. 2007 (47) 1776 - 1786.DOI: 10.1021/ci700107y

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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

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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

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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

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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

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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

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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

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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

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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/

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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

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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

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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

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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

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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

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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

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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

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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

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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+

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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

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13. 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

Andreas Bender, Hamse Y. Mussa and Robert C. Glen
J. Biomol. Scr. 2005 (10) 658 - 666.DOI: 10.1177/1087057105281048

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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

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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

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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

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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

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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

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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 FunctionDownload 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

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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

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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

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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

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2. Molecular Similarity Searching using Atom Environments, Information-Based Feature Selection and a Naïve 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

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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

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Other PublicationsEvent / ReferenceReferenceLink
"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 2003Biosilico, 2003(1), 53-54read (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 PresentationsTitleEventLink
Andreas BenderMerging High-Content Screening and in silico Approaches for Compound Profiling and Mode-of-Action AnalysisBio-IT World Expo 2008, Boston/MA, April 2008n/a
Andreas BenderIn Silico Drug Design: Identification of Active Compounds and the Prediction of On-Target and Off- Target Effects6th Annual Congress: G Protein-Coupled Receptors in Drug Discovery, Berlin, March 2008n/a
Andreas BenderCompound Profiling by Predicting On-Target Activities, Compound Promiscuity and Adverse Drug Reactions3rd CHI Conference on Compound Profiling, Philadelphia/PA, October 2007n/a
Andreas BenderTarget-Prediction for Small Molecules – Know More About On-Target and Off- Target Effects of Your CompoundsMedChem 2007, Boston, September 2007n/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 BenderIn Silico Drug Design: From Virtual Screening and the Prediction of Adverse Drug Reactions to the Shape of Chemical SpaceInternational Conference on Chemoinformatics, Pune, January 2007n/a
Andreas BenderIn Silico Drug Design: Identification of Active Compounds and the Prediction of On-Target and Off-Target EffectsMedChem USA 2006, San Diego, September 2006n/a
Andreas BenderMolecular Similarity - Approaches, Advances and Illusions EuroQSAR 2006, Mediterrenean Sea, September 2006n/a
Andreas Bender, Robert C. GlenMolecular Similarity - Approaches, Advances and Illusions UK QSAR Meeting, Organon, Scotland - October 2005PPT Slides
Andreas Bender, Robert C. GlenNovel Approaches To Molecular Similarity (‘Molecular Similarity Searching Using COSMO Screening Charges’) CompLife, Konstanz, Germany - September 2005PPT Slides
Andreas BenderSimilarity Searching Based on COSMO Screening Charges (And Some Findings On Current Descriptors) International Conference on Chemical Structures, Noordwijkerhout, The Netherlands - June 2005PPT Slides
Andreas BenderNovel Approaches To Molecular Similarity JCF Fruehjahrssymposium, Berlin, Germany - 8 April 2005PPT 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 2004PPT 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 2004PPT 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 2004PPT Slides
Andreas Bender, Hamse Y. Mussa, Stephan Reiling, Robert C. GlenSimilarity searching using Atom Environments, information gain based feature selection and the Naïve Bayesian ClassifierAmerican Chemical Society Meeting, Anaheim, USA - 29 March 2004PPT Slides
Andreas Bender, Hamse Y. Mussa, Stephan Reiling, Robert C. GlenMolecular Similarity Searching Using Atom EnvironmentsPfizer Graduate Symposium, Cambridge, UK - 20 October 2003-
Andreas Bender, Hamse Y. Mussa, Stephan Reiling, Robert C. GlenMolecular Similarity Searching Using Atom EnvironmentsDaylight EuroMUG 2003, Cambridge, UK - 10 October 2003PPT Slides

Theses / Research ProjectsProject TypeLink
New Approaches To Molecular Similarity.PhD Thesis, University of Cambridge, Cambridge, UK, 2005read (2.9 MB PDF)
New Approaches to Molecular SimilartyCPGS (1st year PhD) Thesis (Cambridge University)read (PDF)
Merkmalsextraktion mitochondrialer Targetingsequenzen in Plasmodium falciparumMaster Thesis (German, University of Frankfurt)read (PDF)
Structure Modeling Of AluminosilsesquioxanesBS Project (Trinity College Dublin)read (PDF)
Chemistry of AluminosiloxanesBS Project (Trinity College Dublin)read (PDF)

Poster Presentations / Conference ProceedingsTitleEvent, Date and PlaceLink
Uli Fechner and Andreas BenderBayCATS - Combining the Potency of a Pharmacophore Descriptor With the Power of the Bayes ClassifierMGMS 2005, Dublin, September 2005PPT File
Fiona T. Mc Cahey, Philip M. Marsden, Andreas Bender, Jos W. M. Tissen, Werner Klaffke and Robert C. GlenMolecular Similarity as a guide to Safety PharmacologyMGMS 2005, Dublin, September 2005PPT File
Andreas Bender, Stephan Reiling, Hamse Y. Mussa, Robert C. GlenNovel Molecular Similarity Searching Using Atom Environments, Information-Based Feature Selection and a Naïve Bayesian Classifier23rd SGAI International Conference on Innovative Techniques and Applications of Artificial Intelligence 2003, 15-17 December 2003, Peterhouse College, CambridgePPT File
Andreas Bender, Stephan Reiling, Hamse Y. Mussa, Robert C. GlenNovel Molecular Similarity Searching Using Atom Environments, Information-Based Feature Selection and a Naïve Bayesian ClassifiereCheminformatics 2003, 10 - 14 November 2003 (Web-Based Conference)PPT File
Andreas Bender, Stephan Reiling, Hamse Y. Mussa, Robert C. GlenMolecular Similarity Searching using Atom Environments, Information-Based Feature Selection and a Naïve Bayesian ClassifierGerman Chemical Society Annual Meeting, 7 - 9 October 2003, MunichPPT File
Andreas Bender, Stephan Reiling, Hamse Y. Mussa, Robert C. GlenMolecular Similarity Searching using Atom Environments, Information-Based Feature Selection and a Naïve Bayesian ClassifierRSC/SOCI Medicinal Chemistry Symposium, 8 September 2003, CambridgePPT File

Non-scientific ArticlesJournalLink
Cheminformatics: Your Personal Ticket Into the Thriving Biotech World?Science's NextWaveread(HTML)
Networking Is the Golden Key Science's NextWaveread (HTML)

old stuff