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Data-Driven Drug Discovery and Molecular Informatics

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  • Currently displaying 481 - 500 of 559 publications
A Scenario Implementation in R for SubtypeDiscovery Examplified on Chemoinformatics Data
F Colas, I Meulenbelt, JJ Houwing-Duistermaat, M Kloppenburg, I Watt, SA van Rooden, M Visser, J Marinus, EO Cannon, A Bender, JJ van Hilten, PE Slagboom, JN Kok
– Communications in Computer and Information Science
(2009)
17,
669
(doi: 10.1007/978-3-540-88479-8_48)
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
(doi: 10.1021/ci900190z)
Chemogenomics: Looking at biology through the lens of chemistry
MR Doddareddy, GJP van Westen, E van der Horst, JE Peironcely, F Corthals, AP Ijzerman, M Emmerich, JL Jenkins, A Bender
– Statistical Analysis and Data Mining The ASA Data Science Journal
(2009)
2,
149
(doi: 10.1002/sam.10046)
A quantitative bgl operon model for E. coli requires bglF conformational change for sugar transport
P Chopra, A Bender
– Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
(2009)
5121 LNBI,
1
(doi: 10.1007/978-3-540-88765-2-1)
Multi-parameter phenotypic profiling: Using cellular effects to characterize small-molecule compounds
Y Feng, TJ Mitchison, A Bender, DW Young, JA Tallarico
– Nature Reviews Drug Discovery
(2009)
8,
567
(doi: 10.1038/nrd2876)
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: The ASA Data Science Journal
(2009)
2,
115
(doi: 10.1002/sam.10036)
Enhancing search space diversity in multi-objective evolutionary drug molecule design using niching
JW Kruisselbrink, A Aleman, MTM Emmerich, AP IJzerman, A Bender, T Bäck, E Van Der Horst
– Proceedings of the 11th Annual Genetic and Evolutionary Computation Conference, GECCO-2009
(2009)
217
(doi: 10.1145/1569901.1569932)
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
– J Biomol Screen
(2009)
14,
690
(doi: 10.1177/1087057109335678)
Frequent substructure mining of GPCR ligands
EVD Horst, A Bender, AP Ijzerman
– Chemistry Central Journal
(2009)
3,
p69
(doi: 10.1186/1752-153x-3-s1-p69)
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
(doi: 10.1021/pr8010843)
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
– Journal of medicinal chemistry
(2009)
52,
3103
(doi: 10.1021/jm801546k)
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
(doi: 10.1021/pr900107z)
The discovery of antibacterial agents using diversity-oriented synthesis.
WRJD Galloway, A Bender, M Welch, DR Spring
– Chem Commun (Camb)
(2009)
2446
(doi: 10.1039/b816852k)
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
(doi: 10.1021/ci8003896)
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
– J Chem Inf Model
(2009)
49,
308
(doi: 10.1021/ci800344p)
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
(doi: 10.1021/ci8003896)
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
(doi: 10.1021/ci800379q)
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
(doi: 10.1021/ci800344p)
How Similar Are Similarity Searching Methods? A Principal Component Analysis of Molecular Descriptor Space
A Bender, JL Jenkins, J Scheiber, SCK Sukuru, M Glick, JW Davies
– Journal of Chemical Information and Modeling
(2009)
49,
108
(doi: 10.1021/ci800249s)
Computational methods to support high-content screening: from compound selection and data analysis to postulating target hypotheses.
A Kümmel, D Gabriel, CN Parker, A Bender
– Expert Opinion on Drug Discovery
(2008)
4,
5
(doi: 10.1517/17460440802586434)

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