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Yusuf Hamied Department of Chemistry

 

Publications by Professor Andreas Bender

Experimental Confirmation of New Drug–Target Interactions Predicted by Drug Profile Matching
L Végner, Á Peragovics, L Tombor, B Jelinek, P Czobor, A Bender, Z Simon, A Málnási-Csizmadia
– Journal of Medicinal Chemistry
(2013)
56,
8377
(DOI: 10.1021/jm400813y)
Extensions to In Silico Bioactivity Predictions Using Pathway Annotations and Differential Pharmacology Analysis: Application to <i>Xenopus laevis</i> Phenotypic Readouts
S Liggi, G Drakakis, AE Hendry, KM Hanson, SC Brewerton, GN Wheeler, MJ Bodkin, DA Evans, A Bender
– Molecular informatics
(2013)
32,
1009
(DOI: 10.1002/minf.201300102)
Benchmarking of protein descriptor sets in proteochemometric modeling (part 2): modeling performance of 13 amino acid descriptor sets.
GJ van Westen, RF Swier, I Cortes-Ciriano, JK Wegner, JP Overington, AP Ijzerman, HW van Vlijmen, A Bender
– Journal of cheminformatics
(2013)
5,
42
(DOI: 10.1186/1758-2946-5-42)
Benchmarking of protein descriptor sets in proteochemometric modeling (part 2): modeling performance of 13 amino acid descriptor sets
GJ van Westen, RF Swier, JK Wegner, AP Ijzerman, HW van Vlijmen, A Bender
– J Cheminform
(2013)
5,
42
(DOI: 10.1186/1758-2946-5-42)
Diversity Selection of Compounds Based on 'Protein Affinity Fingerprints' Improves Sampling of <i>Bioactive</i> Chemical Space
HP Nguyen, A Koutsoukas, F Mohd Fauzi, G Drakakis, M Maciejewski, RC Glen, A Bender
– Chemical biology & drug design
(2013)
82,
252
(DOI: 10.1111/cbdd.12155)
In silico target predictions: defining a benchmarking data set and comparison of performance of the multiclass Naïve Bayes and Parzen-Rosenblatt window.
A Koutsoukas, R Lowe, Y Kalantarmotamedi, HY Mussa, W Klaffke, JBO Mitchell, RC Glen, A Bender
– J Chem Inf Model
(2013)
53,
1957
(DOI: 10.1021/ci300435j)
Computer-aided (in silico) approaches in the mode-of-action analysis and safety assessment of Ostarine and 4-methylamphetamine
F Mohd Fauzi, A Koutsoukas, A Cunningham, A Gallegos, R Sedefov, A Bender
– Human Psychopharmacology Clinical and Experimental
(2013)
28,
365
(DOI: 10.1002/hup.2322)
Relating GPCRs pharmacological space based on ligands chemical similarities
A Koutsoukas, R Torella, G Drakakis, A Bender, RC Glen
– Journal of cheminformatics
(2013)
5,
p26
(DOI: 10.1186/1758-2946-5-s1-p26)
Annotating targets with pathways: extending approaches to mode of action analysis
S Liggi, A Koutsoukas, YK Motamedi, RC Glen, A Bender
– Journal of Cheminformatics
(2013)
5,
p15
(DOI: 10.1186/1758-2946-5-s1-p15)
Revised classification of kinases based on bioactivity data: the importance of data density and choice of visualization
S Paricharak, T Klenka, M Augustin, UA Patel, A Bender
– Journal of Cheminformatics
(2013)
5,
p24
(DOI: 10.1186/1758-2946-5-s1-p24)
In silico target prediction: identification of on- and off-targets for crop protection agents
RK Chiddarwar, A Bender, S Rohrer
– Journal of Cheminformatics
(2013)
5,
p18
(DOI: 10.1186/1758-2946-5-s1-p18)
Using machine learning techniques for rationalising phenotypic readouts from a rat sleeping model
G Drakakis, A Koutsoukas, SC Brewerton, DDE Evans, A Bender
– Journal of Cheminformatics
(2013)
5,
p34
(DOI: 10.1186/1758-2946-5-s1-p34)
Chemogenomics approaches to rationalising compound action of traditional Chinese and Ayurvedic medicines
FM Fauzi, A Koutsoukas, R Lowe, K Joshi, T-P Fan, A Bender
– Journal of Cheminformatics
(2013)
5,
p44
(DOI: 10.1186/1758-2946-5-s1-p44)
Experimental validation of in silico target predictions on synergistic protein targets
I Cortes-Ciriano, A Koutsoukas, O Abian, A Bender, A Velazquez-Campoy
– Journal of Cheminformatics
(2013)
5,
p31
(DOI: 10.1186/1758-2946-5-s1-p31)
Significantly improved HIV inhibitor efficacy prediction employing proteochemometric models generated from antivirogram data.
GJP van Westen, A Hendriks, JK Wegner, AP Ijzerman, HWT van Vlijmen, A Bender
– PLoS computational biology
(2013)
9,
e1002899
(DOI: 10.1371/journal.pcbi.1002899)
Chemogenomics approaches to rationalizing the mode-of-action of traditional chinese and ayurvedic medicines
F Mohd Fauzi, A Koutsoukas, R Lowe, K Joshi, T-P Fan, RC Glen, A Bender
– J Chem Inf Model
(2013)
53,
661
(DOI: 10.1021/ci3005513)
Efficient calculation of compound similarity based on maximum common subgraphs and its application to prediction of gene transcript levels
RJPV Berlo, W Winterbach, MJLD Groot, A Bender, PJT Verheijen, MJT Reinders, DD Ridder
– International journal of bioinformatics research and applications
(2013)
9,
407
(DOI: 10.1504/IJBRA.2013.054688)
Experimental validation of in silico target predictions on synergistic protein targets
I Cortes-Ciriano, A Koutsoukas, O Abian, RC Glen, A Velazquez-Campoy, A Bender
– MedChemComm
(2013)
4,
278
(DOI: 10.1039/c2md20286g)
Linking Ayurveda and Western medicine by integrative analysis
FM Fauzi, A Koutsoukas, R Lowe, K Joshi, T-P Fan, RC Glen, A Bender
– Journal of Ayurveda and Integrative Medicine
(2013)
4,
117
(DOI: 10.4103/0975-9476.113882)
Using multiobjective optimization and energy minimization to design an isoform-selective ligand of the 14-3-3 protein
H Sanchez-Faddeev, MTM Emmerich, FJ Verbeek, AH Henry, S Grimshaw, HP Spaink, HW Van Vlijmen, A Bender
– Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
(2012)
7610,
12
(DOI: 10.1007/978-3-642-34032-1_3)

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