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Publications by Dr Andreas Bender

Databases: Compound bioactivities go public
A Bender
– Nature Chemical Biology
(2010)
6,
309
Mining protein dynamics from sets of crystal structures using "consensus structures"
GJP van Westen, JK Wegner, A Bender, AP Ijzerman, HWT van Vlijmen
– Protein Science
(2010)
19,
742
Metabolite identification pipeline based on MS fragmentation
M Rojas-Cherto, JE Peironcely, PT Kasper, A Bender, JL Faulon, T Reijmers, L Coulier, R Vreeken, T Hankemeier
– ABSTR PAP AM CHEM S
(2010)
239,
Knowledge-based and computational approaches to in vitro safety pharmacology
J Scheiber, A Bender, K Azzaoui, J Jenkins
(2010)
43,
297
Predicting the functions of proteins in Protein-Protein Interaction networks from global information
H Rahmani, H Blockeel, A Bender
– PROCEEDINGS OF THE THIRD INTERNATIONAL WORKSHOP ON MACHINE LEARNING IN SYSTEMS BIOLOGY
(2010)
8,
82
Scaffold Diversity Analysis of Compound Daft Sets Using an Entropy-Based Measure
JL Medina-Franco, K Martinez-Mayorga, A Bender, T Scior
– QSAR & Combinatorial Science
(2009)
28,
1551
Alpha shapes applied to molecular shape characterization exhibit novel properties compared to established shape descriptors.
JA Wilson, A Bender, T Kaya, PA Clemons
– Journal of chemical information and modeling
(2009)
49,
2231
Plate-Based Diversity Selection Based on Empirical HTS Data to Enhance the Number of Hits and Their Chemical Diversity
SCK Sukuru, JL Jenkins, REJ Beckwith, J Scheiber, A Bender, D Mikhailov, JW Davies, M Glick
– Journal of biomolecular screening
(2009)
14,
690
Multi-parameter phenotypic profiling: using cellular effects to characterize small-molecule compounds
Y Feng, TJ Mitchison, A Bender, DW Young, JA Tallarico
– Nat Rev Drug Discov
(2009)
8,
567
Fishing the Target of Antitubercular Compounds: In Silico Target Deconvolution Model Development and Validation
P Prathipati, NL Ma, UH Manjunatha, A Bender
– Journal of Proteome Research
(2009)
8,
2788
The discovery of antibacterial agents using diversity-oriented synthesis.
WRJD Galloway, A Bender, M Welch, DR Spring
– Chemical communications (Cambridge, England)
(2009)
2446
Mapping adverse drug reactions in chemical space
J Scheiber, JL Jenkins, SCK Sukuru, A Bender, D Mikhailov, M Milik, K Azzaoui, S Whitebread, J Hamon, L Urban, M Glick, JW Davies
– J Med Chem
(2009)
52,
3103
Use of Ligand Based Models for Protein Domains To Predict Novel Molecular Targets and Applications To Triage Affinity Chromatography Data
A Bender, D Mikhailov, M Glick, J Scheiber, JW Davies, S Cleaver, S Marshall, JA Tallarico, E Harrington, I Cornella-Taracido, JL Jenkins
– Journal of Proteome Research
(2009)
8,
2575
Substructure mining of GPCR ligands reveals activity-class specific functional groups in an unbiased manner
E van der Horst, Y Okuno, A Bender, AP Ijzerman
– J Chem Inf Model
(2009)
49,
348
Gaining insight into off-target mediated effects of drug candidates with a comprehensive systems chemical biology analysis.
J Scheiber, B Chen, M Milik, SCK Sukuru, A Bender, D Mikhailov, S Whitebread, J Hamon, K Azzaoui, L Urban, M Glick, JW Davies, JL Jenkins
– Journal of chemical information and modeling
(2009)
49,
308
Substructure mining of GPCR ligands reveals activity-class specific functional groups in an unbiased manner.
E van der Horst, Y Okuno, A Bender, AP IJzerman
– Journal of chemical information and modeling
(2009)
49,
348
Characterization of Activity Landscapes Using 2D and 3D Similarity Methods: Consensus Activity Cliffs
JL Medina-Franco, K Martínez-Mayorga, A Bender, RM Marín, MA Giulianotti, C Pinilla, RA Houghten
– J Chem Inf Model
(2009)
49,
477
Gaining Insight into Off-Target Mediated Effects of Drug Candidates with a Comprehensive Systems Chemical Biology Analysis.
J Scheiber, B Chen, M Milik, SC Sukuru, A Bender, D Mikhailov, S Whitebread, J Hamon, K Azzaoui, L Urban, M Glick, JW Davies, JL Jenkins
– J Chem Inf Model
(2009)
49,
308
Combining Aggregation with Pareto Optimization: A Case Study in Evolutionary Molecular Design
JW Kruisselbrink, MTM Emmerich, T Back, A Bender, AP IJzerman, E van der Horst
– Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
(2010)
5467,
453
SPREAD-exploiting chemical features that cause differential activity behavior
J Scheiber, JL Jenkins, A Bender, M Milik, D Mikhailov, SCK Sukuru, B Cornett, S Whitebread, L Urban, JW Davies, M Glick
– Statistical Analysis and Data Mining
(2009)
2,
115

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