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Yusuf Hamied Department of Chemistry

 

Publications by Professor Andreas Bender

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 conference on Genetic and evolutionary computation
(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
– Journal of Biomolecular Screening
(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
– J Proteome Res
(2009)
8,
2575
(DOI: 10.1021/pr900107z)
The discovery of antibacterial agents using diversity-oriented synthesis
WRJD Galloway, A Bender, M Welch, DR Spring
– Chemical Communications
(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: <i>Consensus Activity Cliffs</i>
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
– Journal of Chemical Information and Modeling
(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 Opin Drug Discov
(2008)
4,
5
(DOI: 10.1517/17460440802586434)
Ligand-target prediction using winnow and naive bayesian algorithms and the implications of overall performance statistics
F Nigsch, A Bender, JL Jenkins, JBO Mitchell
– Journal of chemical information and modeling
(2008)
48,
2313
(DOI: 10.1021/ci800079x)
COMP 86-"Virtual Fragment Linking": An approach to identify potent binders from low affinity fragment hits
TJ Crisman, A Bender, M Milik, JL Jenkins, J Scheiber, SCK Sukuru, J Fejzo, U Hommel, JW Davies, M Glick
– ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY
(2008)
236,
Diversity‐oriented synthesis
RJ Spandl, M Díaz-Gavilán, KMG O'Connell, GL Thomas, DR Spring
– The Chemical Record
(2008)
8,
129
(DOI: 10.1002/tcr.20144)
Which aspects of HTS are empirically correlated with downstream success?
A Bender, D Bojanic, JW Davies, TJ Crisman, D Mikhailov, J Scheiber, JL Jenkins, Z Deng, WAG Hill, M Popov, E Jacoby, M Glick
– Curr Opin Drug Discov Devel
(2008)
11,
327
Distributed chemical computing using ChemStar: an open source java remote method invocation architecture applied to large scale molecular data from PubChem.
M Karthikeyan, S Krishnan, AK Pandey, A Bender, A Tropsha
– Journal of chemical information and modeling
(2008)
48,
691
(DOI: 10.1021/ci700334f)

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