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ORCIDJohannes Kirchmair
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2020 – today
- 2024
[j35]Ya Chen
, Thomas Seidel, Roxane Axel Jacob, Steffen Hirte, Angelica Mazzolari, Alessandro Pedretti, Giulio Vistoli, Thierry Langer, Filip Miljkovic, Johannes Kirchmair:
Active Learning Approach for Guiding Site-of-Metabolism Measurement and Annotation. J. Chem. Inf. Model. 64(2): 348-358 (2024)- [j34]Hosein Fooladi, Steffen Hirte, Johannes Kirchmair:
Quantifying the Hardness of Bioactivity Prediction Tasks for Transfer Learning. J. Chem. Inf. Model. 64(10): 4031-4046 (2024) - [j33]Matthias Welsch, Steffen Hirte, Johannes Kirchmair:
Deciphering Molecular Embeddings with Centered Kernel Alignment. J. Chem. Inf. Model. 64(19): 7303-7312 (2024) - 2023
- [j32]Magdalena Wiercioch, Johannes Kirchmair:
DNN-PP: A novel Deep Neural Network approach and its applicability in drug-related property prediction. Expert Syst. Appl. 213(Part C): 119055 (2023) - [j31]Karla Gonzalez-Ponce, Carolina Horta Andrade, Fiona M. I. Hunter, Johannes Kirchmair, Karina Martínez-Mayorga, José L. Medina-Franco, Matthias Rarey, Alexander Tropsha, Alexandre Varnek, Barbara Zdrazil:
School of cheminformatics in Latin America. J. Cheminformatics 15(1): 82 (2023) - 2021
- [j30]Fidele Ntie-Kang, Kiran K. Telukunta, Serge A. T. Fobofou, Victor Chukwudi Osamor, Samuel A. Egieyeh, Marilia Valli, Yannick Djoumbou Feunang, Maria Sorokina, Conrad Stork, Neann Mathai, Paul F. Zierep, Ana L. Chávez-Hernández, Miquel Duran-Frigola, Smith B. Babiaka, Romuald Tematio Fouedjou, Donatus B. Eni, Simeon Akame, Augustine B. Arreyetta-Bawak, Oyere T. Ebob, Jonathan A. Metuge, Boris D. Bekono, Mustafa A. Isa, Raphael Onuku, Daniel M. Shadrack, Thommas M. Musyoka, Vaishali M. Patil, Justin J. J. van der Hooft, Vanderlan da Silva Bolzani, José L. Medina-Franco, Johannes Kirchmair, Tilmann Weber, Özlem Tastan Bishop, Marnix H. Medema, Ludger A. Wessjohann, Jutta Ludwig-Müller:
Computational Applications in Secondary Metabolite Discovery (CAiSMD): an online workshop. J. Cheminformatics 13(1): 64 (2021) - [j29]Marina Garcia de Lomana, Andrea Morger, Ulf Norinder, Roland Buesen, Robert Landsiedel, Andrea Volkamer, Johannes Kirchmair, Miriam Mathea:
ChemBioSim: Enhancing Conformal Prediction of In Vivo Toxicity by Use of Predicted Bioactivities. J. Chem. Inf. Model. 61(7): 3255-3272 (2021) - [i1]José L. Medina-Franco, Karina Martínez-Mayorga, Eli Fernández-de Gortari, Johannes Kirchmair, Jürgen Bajorath:
Rationality over fashion and hype in drug design. F1000Research 10: 397 (2021) - 2020
- [j28]Neann Mathai, Ya Chen, Johannes Kirchmair:
Validation strategies for target prediction methods. Briefings Bioinform. 21(3): 791-802 (2020) - [j27]Conrad Stork, Gerd Embruch, Martin Sícho, Christina de Bruyn Kops, Ya Chen, Daniel Svozil, Johannes Kirchmair:
NERDD: a web portal providing access to in silico tools for drug discovery. Bioinform. 36(4): 1291-1292 (2020) - [j26]Ya Chen, Neann Mathai, Johannes Kirchmair:
Scope of 3D Shape-Based Approaches in Predicting the Macromolecular Targets of Structurally Complex Small Molecules Including Natural Products and Macrocyclic Ligands. J. Chem. Inf. Model. 60(6): 2858-2875 (2020)
2010 – 2019
- 2019
- [j25]Nils-Ole Friedrich, Florian Flachsenberg, Agnes Meyder, Kai Sommer, Johannes Kirchmair, Matthias Rarey:
Conformator: A Novel Method for the Generation of Conformer Ensembles. J. Chem. Inf. Model. 59(2): 731-742 (2019) - [j24]Conrad Stork, Ya Chen, Martin Sícho, Johannes Kirchmair:
Hit Dexter 2.0: Machine-Learning Models for the Prediction of Frequent Hitters. J. Chem. Inf. Model. 59(3): 1030-1043 (2019) - [j23]Martin Sícho, Conrad Stork, Angelica Mazzolari, Christina de Bruyn Kops, Alessandro Pedretti, Bernard Testa, Giulio Vistoli, Daniel Svozil, Johannes Kirchmair:
FAME 3: Predicting the Sites of Metabolism in Synthetic Compounds and Natural Products for Phase 1 and Phase 2 Metabolic Enzymes. J. Chem. Inf. Model. 59(8): 3400-3412 (2019) - 2018
- [j22]Ya Chen, Marina Garcia de Lomana, Nils-Ole Friedrich, Johannes Kirchmair:
Characterization of the Chemical Space of Known and Readily Obtainable Natural Products. J. Chem. Inf. Model. 58(8): 1518-1532 (2018) - 2017
- [j21]Nils-Ole Friedrich, Agnes Meyder, Christina de Bruyn Kops, Kai Sommer, Florian Flachsenberg, Matthias Rarey, Johannes Kirchmair:
High-Quality Dataset of Protein-Bound Ligand Conformations and Its Application to Benchmarking Conformer Ensemble Generators. J. Chem. Inf. Model. 57(3): 529-539 (2017) - [j20]Christina de Bruyn Kops, Nils-Ole Friedrich, Johannes Kirchmair:
Alignment-Based Prediction of Sites of Metabolism. J. Chem. Inf. Model. 57(6): 1258-1264 (2017) - [j19]Martin Sícho, Christina de Bruyn Kops, Conrad Stork, Daniel Svozil, Johannes Kirchmair:
FAME 2: Simple and Effective Machine Learning Model of Cytochrome P450 Regioselectivity. J. Chem. Inf. Model. 57(8): 1832-1846 (2017) - [j18]Ya Chen, Christina de Bruyn Kops, Johannes Kirchmair:
Data Resources for the Computer-Guided Discovery of Bioactive Natural Products. J. Chem. Inf. Model. 57(9): 2099-2111 (2017) - [j17]Nils-Ole Friedrich, Christina de Bruyn Kops, Florian Flachsenberg, Kai Sommer, Matthias Rarey, Johannes Kirchmair:
Benchmarking Commercial Conformer Ensemble Generators. J. Chem. Inf. Model. 57(11): 2719-2728 (2017) - 2014
- [j16]Jonathan D. Tyzack, Hamse Y. Mussa, Mark J. Williamson, Johannes Kirchmair, Robert C. Glen:
Cytochrome P450 site of metabolism prediction from 2D topological fingerprints using GPU accelerated probabilistic classifiers. J. Cheminformatics 6(1): 29 (2014) - 2013
- [j15]Johannes Kirchmair, Andrew Howlett, Julio E. Peironcely, Daniel S. Murrell, Mark J. Williamson, Samuel E. Adams, Thomas Hankemeier, Leo van Buren, Guus Duchateau, Werner Klaffke, Robert C. Glen:
Quantifying the shifts in physicochemical property space introduced by the metabolism of small organic molecules. J. Cheminformatics 5(S-1): 12 (2013) - [j14]Johannes Kirchmair, Andrew Howlett, Julio E. Peironcely, Daniel S. Murrell, Mark J. Williamson, Samuel E. Adams, Thomas Hankemeier, Leo van Buren, Guus Duchateau, Werner Klaffke, Robert C. Glen:
How Do Metabolites Differ from Their Parent Molecules and How Are They Excreted? J. Chem. Inf. Model. 53(2): 354-367 (2013) - [j13]Johannes Kirchmair, Mark J. Williamson, Avid M. Afzal, Jonathan D. Tyzack, Alison P. K. Choy, Andrew Howlett, Patrik Rydberg, Robert C. Glen:
FAst MEtabolizer (FAME): A Rapid and Accurate Predictor of Sites of Metabolism in Multiple Species by Endogenous Enzymes. J. Chem. Inf. Model. 53(11): 2896-2907 (2013) - 2012
- [j12]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) - 2010
- [j11]Gudrun M. Spitzer, Mathias Heiss, Martina Mangold, Patrick Markt, Johannes Kirchmair, Gerhard Wolber, Klaus R. Liedl:
One Concept, Three Implementations of 3D Pharmacophore-Based Virtual Screening: Distinct Coverage of Chemical Search Space. J. Chem. Inf. Model. 50(7): 1241-1247 (2010)
2000 – 2009
- 2009
- [j10]Johannes Kirchmair, Simona Distinto, Patrick Markt, Daniela Schuster, Gudrun M. Spitzer, Klaus R. Liedl, Gerhard Wolber:
How To Optimize Shape-Based Virtual Screening: Choosing the Right Query and Including Chemical Information. J. Chem. Inf. Model. 49(3): 678-692 (2009) - [j9]Gudrun M. Spitzer, Bernd Wellenzohn, Patrick Markt, Johannes Kirchmair, Thierry Langer, Klaus R. Liedl:
Hydrogen-Bonding Patterns of Minor Groove-Binder-DNA Complexes Reveal Criteria for Discovery of New Scaffolds. J. Chem. Inf. Model. 49(4): 1063-1069 (2009) - [j8]Pekka Tiikkainen, Patrick Markt, Gerhard Wolber, Johannes Kirchmair, Simona Distinto, Antti Poso, Olli-P. Kallioniemi:
Critical Comparison of Virtual Screening Methods against the MUV Data Set. J. Chem. Inf. Model. 49(10): 2168-2178 (2009) - 2008
- [j7]Johannes Kirchmair, Patrick Markt, Simona Distinto, Gerhard Wolber, Thierry Langer:
Evaluation of the performance of 3D virtual screening protocols: RMSD comparisons, enrichment assessments, and decoy selection - What can we learn from earlier mistakes? J. Comput. Aided Mol. Des. 22(3-4): 213-228 (2008) - [j6]Patrick Markt, Caroline McGoohan, Brian Walker, Johannes Kirchmair, Clemens Feldmann, Gabriella De Martino, Gudrun M. Spitzer, Simona Distinto, Daniela Schuster, Gerhard Wolber, Christian Laggner, Thierry Langer:
Discovery of Novel Cathepsin S Inhibitors by Pharmacophore-Based Virtual High-Throughput Screening. J. Chem. Inf. Model. 48(8): 1693-1705 (2008) - 2007
- [j5]Patrick Markt, Daniela Schuster, Johannes Kirchmair, Christian Laggner, Thierry Langer:
Pharmacophore modeling and parallel screening for PPAR ligands. J. Comput. Aided Mol. Des. 21(10-11): 575-590 (2007) - [j4]Jiabo Li, Tedman Ehlers, Jon M. Sutter, Shikha Varma-O'Brien, Johannes Kirchmair:
CAESAR: A New Conformer Generation Algorithm Based on Recursive Buildup and Local Rotational Symmetry Consideration. J. Chem. Inf. Model. 47(5): 1923-1932 (2007) - [j3]Johannes Kirchmair, Stojanka Ristic, Kathrin Eder, Patrick Markt, Gerhard Wolber, Christian Laggner, Thierry Langer:
Fast and Efficient in Silico 3D Screening: Toward Maximum Computational Efficiency of Pharmacophore-Based and Shape-Based Approaches. J. Chem. Inf. Model. 47(6): 2182-2196 (2007) - 2006
- [j2]Johannes Kirchmair, Gerhard Wolber, Christian Laggner, Thierry Langer:
Comparative Performance Assessment of the Conformational Model Generators Omega and Catalyst: A Large-Scale Survey on the Retrieval of Protein-Bound Ligand Conformations. J. Chem. Inf. Model. 46(4): 1848-1861 (2006) - 2005
- [j1]Johannes Kirchmair, Christian Laggner, Gerhard Wolber, Thierry Langer:
Comparative Analysis of Protein-Bound Ligand Conformations with Respect to Catalyst's Conformational Space Subsampling Algorithms. J. Chem. Inf. Model. 45(2): 422-430 (2005)
Coauthor Index
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