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ORCIDAndreas Bender 0002
Person information
- affiliation: University of Cambridge, UK
Other persons with the same name
- Andreas Bender — disambiguation page
- Andreas Bender 0001
![[0000-0001-5628-8611]](https://dblp.dagstuhl.de/img/orcid-mark.12x12.png "0000-0001-5628-8611")
— LMU München, Department of Statistics, Munich, Germany - Andreas Bender 0003 — LMU München, Department of Neurology, Munich, Germany
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2020 – today
- 2024
[j107]Morgan C. Thomas, Noel M. O'Boyle, Andreas Bender, Chris de Graaf:
MolScore: a scoring, evaluation and benchmarking framework for generative models in de novo drug design. J. Cheminformatics 16(1): 64 (2024)- [j106]Miguel García-Ortegón, Srijit Seal, Carl Rasmussen, Andreas Bender, Sergio Bacallado:
Graph neural processes for molecules: an evaluation on docking scores and strategies to improve generalization. J. Cheminformatics 16(1): 115 (2024) - [j105]Srijit Seal, Ola Spjuth, Layla Hosseini-Gerami, Miguel García-Ortegón, Shantanu Singh, Andreas Bender, Anne E. Carpenter:
Insights into Drug Cardiotoxicity from Biological and Chemical Data: The First Public Classifiers for FDA Drug-Induced Cardiotoxicity Rank. J. Chem. Inf. Model. 64(4): 1172-1186 (2024) - [j104]Koichi Handa, Shunta Sasaki, Satoshi Asano, Michiharu Kageyama, Takeshi Iijima, Andreas Bender:
Prediction of Inhibitory Activity against the MATE1 Transporter via Combined Fingerprint- and Physics-Based Machine Learning Models. J. Chem. Inf. Model. 64(18): 7068-7076 (2024) - [j103]Kamen P. Petrov, Andreas Bender:
An Open-Source Implementation of the Scaffold Identification and Naming System (SCINS) and Example Applications. J. Chem. Inf. Model. 64(20): 7905-7916 (2024) - [j102]S. Sina Ziaee, Hossein Rahmani, Mina Tabatabaei, Anna H. C. Vlot, Andreas Bender:
DCGG: drug combination prediction using GNN and GAE. Prog. Artif. Intell. 13(1): 17-30 (2024) - [i11]Elsa Lawrence, Adham El-Shazly, Srijit Seal, Chaitanya K. Joshi, Pietro Liò, Shantanu Singh, Andreas Bender, Pietro Sormanni, Matthew Greenig:
Understanding Biology in the Age of Artificial Intelligence. CoRR abs/2403.04106 (2024) - 2023
- [j101]Srijit Seal, Hongbin Yang, Maria-Anna Trapotsi, Satvik Singh, Jordi Carreras Puigvert, Ola Spjuth, Andreas Bender:
Merging bioactivity predictions from cell morphology and chemical fingerprint models using similarity to training data. J. Cheminformatics 15(1): 56 (2023) - [j100]Koichi Handa, Morgan C. Thomas, Michiharu Kageyama, Takeshi Iijima, Andreas Bender:
On the difficulty of validating molecular generative models realistically: a case study on public and proprietary data. J. Cheminformatics 15(1): 112 (2023) - [j99]Benoit Baillif, Jason C. Cole, Ilenia Giangreco, Patrick McCabe, Andreas Bender:
Applying atomistic neural networks to bias conformer ensembles towards bioactive-like conformations. J. Cheminformatics 15(1): 124 (2023) - [j98]Georgi K. Kanev, Yaran Zhang, Albert J. Kooistra, Andreas Bender, Rob Leurs, David Bailey, Thomas Würdinger, Chris de Graaf, Iwan J. P. de Esch, Bart A. Westerman:
Predicting the target landscape of kinase inhibitors using 3D convolutional neural networks. PLoS Comput. Biol. 19(9) (2023) - [c9]Arushi G. K. Majha, Ian Stott, Andreas Bender:
On Modelability and Generalizability: Are Machine Learning Models for Drug Synergy Exploiting Artefacts and Biases in Available Data? MLCB 2023: 123-134 - 2022
- [j97]Stephen Bonner, Ian P. Barrett, Cheng Ye, Rowan Swiers, Ola Engkvist, Andreas Bender, Charles Tapley Hoyt, William L. Hamilton:
A review of biomedical datasets relating to drug discovery: a knowledge graph perspective. Briefings Bioinform. 23(6) (2022) - [j96]Milad Allahgholi, Hossein Rahmani, Delaram Javdani, Zahra Sadeghi-Adl, Andreas Bender, Dezsö Módos, Gerhard Weiss:
DDREL: From drug-drug relationships to drug repurposing. Intell. Data Anal. 26(1): 221-237 (2022) - [j95]Morgan C. Thomas, Noel M. O'Boyle, Andreas Bender, Chris de Graaf:
Augmented Hill-Climb increases reinforcement learning efficiency for language-based de novo molecule generation. J. Cheminformatics 14(1): 68 (2022) - [j94]Miguel García-Ortegón, Gregor N. C. Simm, Austin J. Tripp, José Miguel Hernández-Lobato, Andreas Bender, Sergio Bacallado:
DOCKSTRING: Easy Molecular Docking Yields Better Benchmarks for Ligand Design. J. Chem. Inf. Model. 62(15): 3486-3502 (2022) - [i10]Miguel Garcia-Ortegon, Andreas Bender, Sergio Bacallado:
Conditional Neural Processes for Molecules. CoRR abs/2210.09211 (2022) - [i9]Morgan C. Thomas, Noel M. O'Boyle, Andreas Bender, Chris de Graaf:
Re-evaluating sample efficiency in de novo molecule generation. CoRR abs/2212.01385 (2022) - 2021
- [j93]Leen Kalash, Ian Winfield, Dewi Safitri, Marcel Bermudez, Sabrina Carvalho, Robert C. Glen, Graham Ladds, Andreas Bender:
Structure-based identification of dual ligands at the A2AR and PDE10A with anti-proliferative effects in lung cancer cell-lines. J. Cheminformatics 13(1): 17 (2021) - [j92]Morgan C. Thomas, Robert T. Smith, Noel M. O'Boyle, Chris de Graaf, Andreas Bender:
Comparison of structure- and ligand-based scoring functions for deep generative models: a GPCR case study. J. Cheminformatics 13(1): 39 (2021) - [j91]Lewis H. Mervin, Maria-Anna Trapotsi, Avid M. Afzal, Ian P. Barrett, Andreas Bender, Ola Engkvist:
Probabilistic Random Forest improves bioactivity predictions close to the classification threshold by taking into account experimental uncertainty. J. Cheminformatics 13(1): 62 (2021) - [j90]Maria-Anna Trapotsi, Lewis H. Mervin, Avid M. Afzal, Noé Sturm, Ola Engkvist, Ian P. Barrett, Andreas Bender:
Comparison of Chemical Structure and Cell Morphology Information for Multitask Bioactivity Predictions. J. Chem. Inf. Model. 61(3): 1444-1456 (2021) - [i8]Stephen Bonner, Ian P. Barrett, Cheng Ye, Rowan Swiers, Ola Engkvist, Andreas Bender, William L. Hamilton:
A Review of Biomedical Datasets Relating to Drug Discovery: A Knowledge Graph Perspective. CoRR abs/2102.10062 (2021) - [i7]Miguel García-Ortegón, Gregor N. C. Simm, Austin J. Tripp, José Miguel Hernández-Lobato, Andreas Bender, Sergio Bacallado:
DOCKSTRING: easy molecular docking yields better benchmarks for ligand design. CoRR abs/2110.15486 (2021) - 2020
- [j89]Hamid Bashiri, Hossein Rahmani, Vahid Bashiri, Dezsö Módos, Andreas Bender:
EMDIP: An Entropy Measure to Discover Important Proteins in PPI networks. Comput. Biol. Medicine 120: 103740 (2020) - [j88]Ctibor Skuta, Isidro Cortes-Ciriano, Wim Dehaen, Pavel Kríz, Gerard J. P. van Westen, Igor V. Tetko, Andreas Bender, Daniel Svozil:
QSAR-derived affinity fingerprints (part 1): fingerprint construction and modeling performance for similarity searching, bioactivity classification and scaffold hopping. J. Cheminformatics 12(1): 39 (2020) - [j87]Isidro Cortés-Ciriano, Ctibor Skuta, Andreas Bender, Daniel Svozil:
QSAR-derived affinity fingerprints (part 2): modeling performance for potency prediction. J. Cheminformatics 12(1): 41 (2020) - [j86]Lewis H. Mervin, Avid M. Afzal, Ola Engkvist, Andreas Bender:
Comparison of Scaling Methods to Obtain Calibrated Probabilities of Activity for Protein-Ligand Predictions. J. Chem. Inf. Model. 60(10): 4546-4559 (2020) - [j85]Iñigo Ayestaran, Ana Galhoz, Elmar Spiegel, Ben Sidders, Jonathan R. Dry, Frank Dondelinger, Andreas Bender, Ultan McDermott, Francesco Iorio, Michael P. Menden:
Identification of Intrinsic Drug Resistance and Its Biomarkers in High-Throughput Pharmacogenomic and CRISPR Screens. Patterns 1(5): 100065 (2020)
2010 – 2019
- 2019
- [j84]Erin Oerton, Ian Roberts, Patrick S. H. Lewis, Tim Guilliams, Andreas Bender:
Understanding and predicting disease relationships through similarity fusion. Bioinform. 35(7): 1213-1220 (2019) - [j83]Chad H. G. Allen, Lewis H. Mervin, Samar Y. Mahmoud, Andreas Bender:
Leveraging heterogeneous data from GHS toxicity annotations, molecular and protein target descriptors and Tox21 assay readouts to predict and rationalise acute toxicity. J. Cheminformatics 11(1): 36:1-36:19 (2019) - [j82]Isidro Cortes-Ciriano, Andreas Bender:
KekuleScope: prediction of cancer cell line sensitivity and compound potency using convolutional neural networks trained on compound images. J. Cheminformatics 11(1): 41:1-41:16 (2019) - [j81]Isidro Cortés-Ciriano, Andreas Bender:
Deep Confidence: A Computationally Efficient Framework for Calculating Reliable Prediction Errors for Deep Neural Networks. J. Chem. Inf. Model. 59(3): 1269-1281 (2019) - [j80]Isidro Cortés-Ciriano, Andreas Bender:
Reliable Prediction Errors for Deep Neural Networks Using Test-Time Dropout. J. Chem. Inf. Model. 59(7): 3330-3339 (2019) - [i6]Isidro Cortes-Ciriano, Andreas Bender:
Reliable Prediction Errors for Deep Neural Networks Using Test-Time Dropout. CoRR abs/1904.06330 (2019) - [i5]Isidro Cortés-Ciriano, Andreas Bender:
Concepts and Applications of Conformal Prediction in Computational Drug Discovery. CoRR abs/1908.03569 (2019) - 2018
- [j79]Shardul Paricharak, Oscar Méndez-Lucio, Aakash Chavan Ravindranath, Andreas Bender, Adriaan P. IJzerman, Gerard J. P. van Westen:
Data-driven approaches used for compound library design, hit triage and bioactivity modeling in high-throughput screening. Briefings Bioinform. 19(2): 277-285 (2018) - [j78]Lewis H. Mervin, Krishna C. Bulusu, Leen Kalash, Avid M. Afzal, Fredrik Svensson, Mike A. Firth, Ian P. Barrett, Ola Engkvist, Andreas Bender:
Orthologue chemical space and its influence on target prediction. Bioinform. 34(1): 72-79 (2018) - [j77]Kristina Preuer, Richard P. I. Lewis, Sepp Hochreiter, Andreas Bender, Krishna C. Bulusu, Günter Klambauer:
DeepSynergy: predicting anti-cancer drug synergy with Deep Learning. Bioinform. 34(9): 1538-1546 (2018) - [j76]Fredrik Svensson, Avid M. Afzal, Ulf Norinder, Andreas Bender:
Maximizing gain in high-throughput screening using conformal prediction. J. Cheminformatics 10(1): 7:1-7:10 (2018) - [j75]Yue Kong, Andreas Bender, Aixia Yan:
Identification of Novel Aurora Kinase A (AURKA) Inhibitors via Hierarchical Ligand-Based Virtual Screening. J. Chem. Inf. Model. 58(1): 36-47 (2018) - [j74]Fredrik Svensson, Natália Aniceto, Ulf Norinder, Isidro Cortes-Ciriano, Ola Spjuth, Lars Carlsson, Andreas Bender:
Conformal Regression for Quantitative Structure-Activity Relationship Modeling - Quantifying Prediction Uncertainty. J. Chem. Inf. Model. 58(5): 1132-1140 (2018) - [j73]Kathryn A. Giblin, Samantha J. Hughes, Helen Boyd, Pia Hansson, Andreas Bender:
Prospectively Validated Proteochemometric Models for the Prediction of Small-Molecule Binding to Bromodomain Proteins. J. Chem. Inf. Model. 58(9): 1870-1888 (2018) - [j72]Isidro Cortés-Ciriano, Nicholas C. Firth, Andreas Bender, Oliver P. Watson:
Discovering Highly Potent Molecules from an Initial Set of Inactives Using Iterative Screening. J. Chem. Inf. Model. 58(9): 2000-2014 (2018) - [i4]Isidro Cortes-Ciriano, Andreas Bender:
Deep Confidence: A Computationally Efficient Framework for Calculating Reliable Errors for Deep Neural Networks. CoRR abs/1809.09060 (2018) - [i3]Isidro Cortes-Ciriano, Andreas Bender:
KekuleScope: improved prediction of cancer cell line sensitivity using convolutional neural networks trained on compound images. CoRR abs/1811.09036 (2018) - 2017
- [j71]Leen Kalash, Cristina Val, Jhonny Azuaje, Maria Isabel Loza, Fredrik Svensson, Azedine Zoufir, Lewis H. Mervin, Graham Ladds, José M. Brea, Robert C. Glen, Eddy Sotelo, Andreas Bender:
Computer-aided design of multi-target ligands at A1R, A2AR and PDE10A, key proteins in neurodegenerative diseases. J. Cheminformatics 9(1): 67:1-67:19 (2017) - [j70]Fredrik Svensson, Ulf Norinder, Andreas Bender:
Improving Screening Efficiency through Iterative Screening Using Docking and Conformal Prediction. J. Chem. Inf. Model. 57(3): 439-444 (2017) - [j69]Xianjun Fu, Lewis H. Mervin, Xuebo Li, Huayun Yu, Jiaoyang Li, Siti Zuraidah Mohamad Zobir, Azedine Zoufir, Yang Zhou, Yongmei Song, Zhenguo Wang, Andreas Bender:
Toward Understanding the Cold, Hot, and Neutral Nature of Chinese Medicines Using in Silico Mode-of-Action Analysis. J. Chem. Inf. Model. 57(3): 468-483 (2017) - [j68]Stephanie K. Ashenden, Thierry Kogej, Ola Engkvist, Andreas Bender:
Innovation in Small-Molecule-Druggable Chemical Space: Where are the Initial Modulators of New Targets Published? J. Chem. Inf. Model. 57(11): 2741-2753 (2017) - 2016
- [j67]Isidro Cortes-Ciriano, Gerard J. P. van Westen, Guillaume Bouvier, Michael Nilges, John P. Overington, Andreas Bender, Thérèse E. Malliavin:
Improved large-scale prediction of growth inhibition patterns using the NCI60 cancer cell line panel. Bioinform. 32(1): 85-95 (2016) - [j66]Hossein Rahmani, Gerhard Weiss, Oscar Méndez-Lucio, Andreas Bender:
ARWAR: A network approach for predicting Adverse Drug Reactions. Comput. Biol. Medicine 68: 101-108 (2016) - [j65]Hossein Rahmani, Hendrik Blockeel, Andreas Bender:
Using a Human Drug Network for generating novel hypotheses about drugs. Intell. Data Anal. 20(1): 183-197 (2016) - [j64]Natália Aniceto, Alex Alves Freitas, Andreas Bender, Taravat Ghafourian:
A novel applicability domain technique for mapping predictive reliability across the chemical space of a QSAR: reliability-density neighbourhood. J. Cheminformatics 8(1): 69:1-69:20 (2016) - [j63]Shardul Paricharak, Adriaan P. IJzerman, Jeremy L. Jenkins, Andreas Bender, Florian Nigsch:
Data-Driven Derivation of an "Informer Compound Set" for Improved Selection of Active Compounds in High-Throughput Screening. J. Chem. Inf. Model. 56(9): 1622-1630 (2016) - 2015
- [j62]Isidro Cortes-Ciriano, Gerard J. P. van Westen, Daniel S. Murrell, Eelke B. Lenselink, Andreas Bender, Therese E. Malliavin:
Applications of proteochemometrics - from species extrapolation to cell line sensitivity modelling. BMC Bioinform. 16(S-3): A4 (2015) - [j61]Hossein Rahmani, Hendrik Blockeel, Andreas Bender:
Using a Human Disease Network for augmenting prior knowledge about diseases. Intell. Data Anal. 19(4): 897-916 (2015) - [j60]Isidro Cortes-Ciriano, Daniel S. Murrell, Gerard J. P. van Westen, Andreas Bender, Thérèse E. Malliavin:
Prediction of the potency of mammalian cyclooxygenase inhibitors with ensemble proteochemometric modeling. J. Cheminformatics 7: 1 (2015) - [j59]Shardul Paricharak, Isidro Cortes-Ciriano, Adriaan P. IJzerman, Therese E. Malliavin, Andreas Bender:
Proteochemometric modelling coupled to in silico target prediction: an integrated approach for the simultaneous prediction of polypharmacology and binding affinity/potency of small molecules. J. Cheminformatics 7: 15 (2015) - [j58]Avid M. Afzal, Hamse Y. Mussa, Richard E. Turner, Andreas Bender, Robert C. Glen:
A multi-label approach to target prediction taking ligand promiscuity into account. J. Cheminformatics 7: 24:1-24:14 (2015) - [j57]Lora Mak, David Marcus, Andrew Howlett, Galina Yarova, Guus Duchateau, Werner Klaffke, Andreas Bender, Robert C. Glen:
Metrabase: a cheminformatics and bioinformatics database for small molecule transporter data analysis and (Q)SAR modeling. J. Cheminformatics 7: 31:1-31:12 (2015) - [j56]Richard Lewis, Rajarshi Guha, Tamás Korcsmáros, Andreas Bender:
Synergy Maps: exploring compound combinations using network-based visualization. J. Cheminformatics 7: 36:1-36:11 (2015) - [j55]Daniel S. Murrell, Isidro Cortes-Ciriano, Gerard J. P. van Westen, Ian Stott, Andreas Bender, Thérèse E. Malliavin, Robert C. Glen:
Chemically Aware Model Builder (camb): an R package for property and bioactivity modelling of small molecules. J. Cheminformatics 7: 45:1-45:10 (2015) - [j54]Lewis H. Mervin, Avid M. Afzal, Georgios Drakakis, Richard Lewis, Ola Engkvist, Andreas Bender:
Target prediction utilising negative bioactivity data covering large chemical space. J. Cheminformatics 7: 51:1-51:16 (2015) - [j53]Oscar Méndez-Lucio, Albert J. Kooistra, Chris de Graaf, Andreas Bender, José L. Medina-Franco:
Analyzing Multitarget Activity Landscapes Using Protein-Ligand Interaction Fingerprints: Interaction Cliffs. J. Chem. Inf. Model. 55(2): 251-262 (2015) - [j52]Isidro Cortes-Ciriano, Andreas Bender, Thérèse E. Malliavin:
Comparing the Influence of Simulated Experimental Errors on 12 Machine Learning Algorithms in Bioactivity Modeling Using 12 Diverse Data Sets. J. Chem. Inf. Model. 55(7): 1413-1425 (2015) - [j51]Isidro Cortes-Ciriano, Andreas Bender:
Improved Chemical Structure-Activity Modeling Through Data Augmentation. J. Chem. Inf. Model. 55(12): 2682-2692 (2015) - 2014
- [j50]Isidro Cortes-Ciriano, Gerard J. P. van Westen, Eelke B. Lenselink, Daniel S. Murrell, Andreas Bender, Thérèse E. Malliavin:
Proteochemometric modeling in a Bayesian framework. J. Cheminformatics 6(1): 35 (2014) - [j49]Alexios Koutsoukas, Shardul Paricharak, Warren R. J. D. Galloway, David R. Spring, Adriaan P. IJzerman, Robert C. Glen, David Marcus, Andreas Bender:
How Diverse Are Diversity Assessment Methods? A Comparative Analysis and Benchmarking of Molecular Descriptor Space. J. Chem. Inf. Model. 54(1): 230-242 (2014) - [j48]Alexios Koutsoukas, Robert Lowe, Yasaman KalantarMotamedi, Hamse Y. Mussa, Werner Klaffke, John B. O. Mitchell, Robert C. Glen, Andreas Bender:
Erratum for "In Silico Target Predictions: Defining a Benchmarking Data Set and Comparison of Performance of the Multiclass Naı̈ve Bayes and Parzen-Rosenblatt Window". J. Chem. Inf. Model. 54(7): 2180-2182 (2014) - [i2]Avid M. Afzal, Hamse Y. Mussa, Richard E. Turner, Andreas Bender, Robert C. Glen:
Target Fishing: A Single-Label or Multi-Label Problem? CoRR abs/1411.6285 (2014) - 2013
- [j47]Rogier J. P. van Berlo, Wynand Winterbach, Marco J. L. de Groot, Andreas Bender, Peter J. T. Verheijen, Marcel J. T. Reinders, Dick de Ridder:
Efficient calculation of compound similarity based on maximum common subgraphs and its application to prediction of gene transcript levels. Int. J. Bioinform. Res. Appl. 9(4): 407-432 (2013) - [j46]Sonia Liggi, Alexios Koutsoukas, Yasaman Motamedi, Robert C. Glen, Andreas Bender:
Annotating targets with pathways: extending approaches to mode of action analysis. J. Cheminformatics 5(S-1): 15 (2013) - [j45]Shardul Paricharak, Tom Klenka, Martin Augustin, Umesh A. Patel, Andreas Bender:
Revised classification of kinases based on bioactivity data: the importance of data density and choice of visualization. J. Cheminformatics 5(S-1): 24 (2013) - [j44]Alexios Koutsoukas, Rubben Torella, George Drakakis, Andreas Bender, Robert C. Glen:
Relating GPCRs pharmacological space based on ligands chemical similarities. J. Cheminformatics 5(S-1): 26 (2013) - [j43]Isidro Cortes-Ciriano, Alexios Koutsoukas, Olga Abian, Andreas Bender, Adrián Velázquez-Campoy:
Experimental validation of in silico target predictions on synergistic protein targets. J. Cheminformatics 5(S-1): 31 (2013) - [j42]Georgios Drakakis, Alexios Koutsoukas, Suzanne Clare Brewerton, David A. Evans, Andreas Bender:
Using machine learning techniques for rationalising phenotypic readouts from a rat sleeping model. J. Cheminformatics 5(S-1): 34 (2013) - [j41]Gerard J. P. van Westen, Remco F. Swier, Jörg K. Wegner, Adriaan P. IJzerman, Herman W. T. van Vlijmen, Andreas Bender:
Benchmarking of protein descriptor sets in proteochemometric modeling (part 1): comparative study of 13 amino acid descriptor sets. J. Cheminformatics 5: 41 (2013) - [j40]Gerard J. P. van Westen, Remco F. Swier, Isidro Cortes-Ciriano, Jörg K. Wegner, John P. Overington, Adriaan P. IJzerman, Herman W. T. van Vlijmen, Andreas Bender:
Benchmarking of protein descriptor sets in proteochemometric modeling (part 2): modeling performance of 13 amino acid descriptor sets. J. Cheminformatics 5: 42 (2013) - [j39]Fazlin Fauzi, Alexios Koutsoukas, Robert Lowe, Kalpana Joshi, Tai-Ping Fan, Andreas Bender:
Chemogenomics approaches to rationalising compound action of traditional Chinese and Ayurvedic medicines. J. Cheminformatics 5(S-1): 44 (2013) - [j38]Shardul Paricharak, Tom Klenka, Martin Augustin, Umesh A. Patel, Andreas Bender:
Are phylogenetic trees suitable for chemogenomics analyses of bioactivity data sets: the importance of shared active compounds and choosing a suitable data embedding method, as exemplified on Kinases. J. Cheminformatics 5: 49 (2013) - [j37]Fazlin Fauzi, Alexios Koutsoukas, Robert Lowe, Kalpana Joshi, Tai-Ping Fan, Robert C. Glen, Andreas Bender:
Chemogenomics Approaches to Rationalizing the Mode-of-Action of Traditional Chinese and Ayurvedic Medicines. J. Chem. Inf. Model. 53(3): 661-673 (2013) - [j36]Alexios Koutsoukas, Robert Lowe, Yasaman KalantarMotamedi, Hamse Y. Mussa, Werner Klaffke, John B. O. Mitchell, Robert C. Glen, Andreas Bender:
In Silico Target Predictions: Defining a Benchmarking Data Set and Comparison of Performance of the Multiclass Naïve Bayes and Parzen-Rosenblatt Window. J. Chem. Inf. Model. 53(8): 1957-1966 (2013) - [j35]Gerard J. P. van Westen, Alwin Hendriks, Jörg K. Wegner, Adriaan P. IJzerman, Herman W. T. van Vlijmen, Andreas Bender:
Significantly Improved HIV Inhibitor Efficacy Prediction Employing Proteochemometric Models Generated From Antivirogram Data. PLoS Comput. Biol. 9(2) (2013) - [i1]Andreas Bender, Hinrich W. H. Göhlmann, Sepp Hochreiter, Ziv Shkedy:
Computational Methods Aiding Early-Stage Drug Design (Dagstuhl Seminar 13212). Dagstuhl Reports 3(5): 78-94 (2013) - 2012
- [j34]Jörg K. Wegner, Aaron D. Sterling, Rajarshi Guha, Andreas Bender, Jean-Loup Faulon, Janna Hastings, Noel M. O'Boyle, John P. Overington, Herman van Vlijmen, Egon L. Willighagen:
Cheminformatics. Commun. ACM 55(11): 65-75 (2012) - [j33]Florian D. Roessler, Oliver Korb, Andreas Bender, Werner Maentele, Peter J. Bond:
Molecular dynamics simulations and docking of non-nucleoside reverse transcriptase inhibitors (NNRTIs): a possible approach to personalized HIV treatment. J. Cheminformatics 4(S-1): 32 (2012) - [j32]Johannes Kirchmair, Mark J. Williamson, Jonathan D. Tyzack, Lu Tan, Peter J. Bond, Andreas Bender, Robert C. Glen:
Computational Prediction of Metabolism: Sites, Products, SAR, P450 Enzyme Dynamics, and Mechanisms. J. Chem. Inf. Model. 52(3): 617-648 (2012) - [j31]Thomas Scior, Andreas Bender, Gary Tresadern, José L. Medina-Franco, Karina Martínez-Mayorga, Thierry Langer, Karina Cuanalo-Contreras, Dimitris K. Agrafiotis:
Recognizing Pitfalls in Virtual Screening: A Critical Review. J. Chem. Inf. Model. 52(4): 867-881 (2012) - [j30]Eelke van der Horst, Patricia Marqués-Gallego, Thea Mulder-Krieger, Jacobus van Veldhoven, Johannes W. Kruisselbrink, Alexander Aleman, Michael T. M. Emmerich, Johannes Brussee, Andreas Bender, Adriaan P. IJzerman:
Multi-Objective Evolutionary Design of Adenosine Receptor Ligands. J. Chem. Inf. Model. 52(7): 1713-1721 (2012) - [j29]Hossein Rahmani, Hendrik Blockeel, Andreas Bender:
Predicting Genes Involved in Human Cancer Using Network Contextual Information. J. Integr. Bioinform. 9(1) (2012) - [c8]Hernando Sanchez-Faddeev, Michael T. M. Emmerich, Fons J. Verbeek, Andrew H. Henry, Simon Grimshaw, Herman P. Spaink, Herman W. T. van Vlijmen, Andreas Bender:
Using Multiobjective Optimization and Energy Minimization to Design an Isoform-Selective Ligand of the 14-3-3 Protein. ISoLA (2) 2012: 12-24 - 2011
- [j28]Iurii Sushko, Sergii Novotarskyi, Robert Körner, Anil Kumar Pandey, Matthias Rupp, Wolfram Teetz, Stefan Brandmaier, Ahmed Abdelaziz, Volodymyr V. Prokopenko, Vsevolod Yu. Tanchuk, Roberto Todeschini, Alexandre Varnek, Gilles Marcou, Peter Ertl, Vladimir Potemkin, Maria A. Grishina, Johann Gasteiger, Christof H. Schwab, Igor I. Baskin, Vladimir A. Palyulin, Eugene V. Radchenko, William J. Welsh, Vladyslav V. Kholodovych, Dmitriy Chekmarev, Artem Cherkasov, João Aires-de-Sousa, Qing-You Zhang, Andreas Bender, Florian Nigsch, Luc Patiny, Antony J. Williams, Valery Tkachenko, Igor V. Tetko:
Online chemical modeling environment (OCHEM): web platform for data storage, model development and publishing of chemical information. J. Comput. Aided Mol. Des. 25(6): 533-554 (2011) - [j27]Iurii Sushko, Anil Kumar Pandey, Sergii Novotarskyi, Robert Körner, Matthias Rupp, Wolfram Teetz, Stefan Brandmaier, Ahmed Abdelaziz, Volodymyr V. Prokopenko, Vsevolod Yu. Tanchuk, Roberto Todeschini, Alexandre Varnek, Gilles Marcou, Peter Ertl, Vladimir Potemkin, Maria A. Grishina, Johann Gasteiger, Igor I. Baskin, Vladimir A. Palyulin, Eugene V. Radchenko, William J. Welsh, Vladyslav V. Kholodovych, Dmitriy Chekmarev, Artem Cherkasov, João Aires-de-Sousa, Qing-You Zhang, Andreas Bender, Florian Nigsch, Luc Patiny, Antony J. Williams, Valery Tkachenko, Igor V. Tetko:
Online chemical modeling environment (OCHEM): web platform for data storage, model development and publishing of chemical information. J. Cheminformatics 3(S-1): 20 (2011) - [j26]Zhi Wang, Yuanying Chen, Hu Liang, Andreas Bender, Robert C. Glen, Aixia Yan:
P-glycoprotein Substrate Models Using Support Vector Machines Based on a Comprehensive Data set. J. Chem. Inf. Model. 51(6): 1447-1456 (2011) - [c7]Hossein Rahmani, Hendrik Blockeel, Andreas Bender:
Collaboration-Based Function Prediction in Protein-Protein Interaction Networks. IDA 2011: 318-327 - 2010
- [j25]Eelke van der Horst, Julio E. Peironcely, Adriaan P. IJzerman, Margot W. Beukers, Jonathan Robert Lane, Herman W. T. van Vlijmen, Michael T. M. Emmerich, Yasushi Okuno, Andreas Bender:
A novel chemogenomics analysis of G protein-coupled receptors (GPCRs) and their ligands: a potential strategy for receptor de-orphanization. BMC Bioinform. 11: 316 (2010) - [j24]Gerard J. P. van Westen, Jörg K. Wegner, Adriaan P. IJzerman, Herman W. T. van Vlijmen, Andreas Bender:
Molecular bioactivity extrapolation to novel targets by support vector machines. J. Cheminformatics 2(S-1): 3 (2010) - [j23]Olaf van den Hoven, Gerard J. P. van Westen, Andreas Bender:
Predicting the binding type of compounds on the 4 adenosine receptors using proteochemometric models. J. Cheminformatics 2(S-1): 16 (2010) - [j22]Julio E. Peironcely, Andreas Bender, Miguel Rojas-Chertó, Theo H. Reijmers, Leon Coulier, Thomas Hankemeier:
Expanding and understanding metabolite space. J. Cheminformatics 2(S-1): 39 (2010) - [j21]