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Department of Chemistry

 

Publications by Dr Andreas Bender

Chemogenomic data analysis: prediction of small-molecule targets and the advent of biological fingerprint.
A Bender, DW Young, JL Jenkins, M Serrano, D Mikhailov, PA Clemons, JW Davies
– Comb Chem High Throughput Screen
(2007)
10,
719
(DOI: 10.2174/138620707782507313)
Side effect profile prediction: Computational tackling of big pharma's worst nightmare at an early stage
J Scheiber, JL Jenkins, A Bender, S Whitebread, J Hamon, L Urban, K Azzaoui, JH Nettles, M Glick, JW Davies
– ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY
(2007)
234,
"Phylochemical Tree" for drug targets: Putting biological activities into context via ligand-based similarity measures
A Bender, JL Jenkins, JW Davies
– ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY
(2007)
234,
COMP 158-Automated combinatorial alignment for 3-D similarity searching
JH Nettles, JL Jenkins, Z Deng, A Bender, JW Davies, M Glick
– ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY
(2007)
234,
Prediction of small molecule targets based on protein domains: Extrapolation into unknown target space
JL Jenkins, A Bender, D Mikhailov
– ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY
(2007)
234,
COMP 495-Tautomers, conformers, and computation of chemical similarity
JH Nettles, JL Jenkins, Z Deng, A Bender, J Scheiber, JW Davies, M Glick
– ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY
(2007)
234,
Understanding False Positives in Reporter Gene Assays:  in Silico Chemogenomics Approaches To Prioritize Cell-Based HTS Data
TJ Crisman, CN Parker, JL Jenkins, J Scheiber, M Thoma, ZB Kang, R Kim, A Bender, JH Nettles, JW Davies, M Glick
– J Chem Inf Model
(2007)
47,
1319
(DOI: 10.1021/ci6005504)
Analysis of pharmacology data and the prediction of adverse drug reactions and off-target effects from chemical structure.
A Bender, J Scheiber, M Glick, JW Davies, K Azzaoui, J Hamon, L Urban, S Whitebread, JL Jenkins
– ChemMedChem
(2007)
2,
861
(DOI: 10.1002/cmdc.200700026)
Modeling promiscuity based on in vitro safety pharmacology profiling data.
K Azzaoui, J Hamon, B Faller, S Whitebread, E Jacoby, A Bender, JL Jenkins, L Urban
– ChemMedChem
(2007)
2,
874
(DOI: 10.1002/cmdc.200700036)
Support vector inductive logic programming outperforms the Naive Bayes Classifier and inductive logic programming for the classification of bioactive chemical compounds
EO Cannon, A Amini, A Bender, MJE Sternberg, SH Muggleton, RC Glen, JBO Mitchell
– J Comput Aided Mol Des
(2007)
21,
269
(DOI: 10.1007/s10822-007-9113-3)
"Plate cherry picking": a novel semi-sequential screening paradigm for cheaper, faster, information-rich compound selection.
TJ Crisman, JL Jenkins, CN Parker, WAG Hill, A Bender, Z Deng, JH Nettles, JW Davies, M Glick
– Journal of Biomolecular Screening
(2007)
12,
320
(DOI: 10.1177/1087057107299427)
Evolved cellular automata for protein secondary structure prediction imitate the determinants for folding observed in nature.
P Chopra, A Bender
– In Silico Biol
(2007)
7,
87
Bridging chemical and biological space: "Target fishing" using 2D and 3D molecular descriptors
JH Nettles, JL Jenkins, A Bender, Z Deng, JW Davies, M Glick
– J Med Chem
(2006)
49,
6802
(DOI: 10.1021/jm060902w)
Chemoinformatics-based classification of prohibited substances employed for doping in sport.
EO Cannon, A Bender, DS Palmer, JBO Mitchell
– J Chem Inf Model
(2006)
46,
2369
(DOI: 10.1021/ci0601160)
"Bayes affinity fingerprints" improve retrieval rates in virtual screening and define orthogonal bioactivity space: when are multitarget drugs a feasible concept?
A Bender, JL Jenkins, M Glick, Z Deng, JH Nettles, JW Davies
– J Chem Inf Model
(2006)
46,
2445
(DOI: 10.1021/ci600197y)
Melting point prediction employing k-nearest neighbor algorithms and genetic parameter optimization.
F Nigsch, A Bender, B van Buuren, J Tissen, E Nigsch, JBO Mitchell
– J Chem Inf Model
(2006)
46,
2412
(DOI: 10.1021/ci060149f)
Bridging chemical and biological space: "Target Fishing" using 2D and 3D molecular descriptors
JH Nettles, JL Jenkins, A Bender, Z Deng, JW Davies, M Glick
– ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY
(2006)
232,
293
Analysis of Activity Space by Fragment Fingerprints, 2D Descriptors, and Multitarget Dependent Transformation of 2D Descriptors
A Givehchi, A Bender, RC Glen
– J Chem Inf Model
(2006)
46,
1078
(DOI: 10.1021/ci0500233)
Circular fingerprints: Flexible molecular descriptors with applications from physical chemistry to ADME (vol 9, pg 199, 2006)
RC Glen, A Bender, CH Arnby, L Carlsson, S Boyer, J Smith
– IDRUGS
(2006)
9,
311
Virtual screening: The king (quite often) has no clothes
RC Glen, A Bender
– ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY
(2006)
231,

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