Johannes Kirchmair

44 papers Journal 44

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	FAME3R: an efficient, practical and reliable open-source tool for predicting phase 1 and phase 2 sites of metabolism. J. Cheminformatics Roxane Axel Jacob, Leo Gaskin, Thomas Seidel, Ya Chen, Angelica Mazzolari, Johannes Kirchmair
2025	J	`jnl`	Automated Annotation of Sites of Metabolism from Biotransformation Data. J. Chem. Inf. Model. Roxane Axel Jacob, Angelica Mazzolari, Johannes Kirchmair
2025	J	`jnl`	E-GuARD: expert-guided augmentation for the robust detection of compounds interfering with biological assays. J. Cheminformatics Vincenzo Palmacci, Yasmine Nahal, Matthias Welsch, Ola Engkvist, Samuel Kaski, Johannes Kirchmair
2025	J	`jnl`	Evaluating Machine Learning Models for Molecular Property Prediction: Performance and Robustness on Out-of-Distribution Data. J. Chem. Inf. Model. Hosein Fooladi, Thi Ngoc Lan Vu, Miriam Mathea, Johannes Kirchmair
2025	J	`jnl`	Integrated Virtual Screening Approach Identifies New CYP19A1 Inhibitors. J. Chem. Inf. Model. Sijie Liu, Jie Wu, Ya Chen, Clemens Alexander Wolf, Matthias Bureik, Johannes Kirchmair, Mario Andrea Marchisio, Gerhard Wolber
2025	J	`jnl`	Integrating Machine Learning-Based Pose Sampling with Established Scoring Functions for Virtual Screening. J. Chem. Inf. Model. Thi Ngoc Lan Vu, Hosein Fooladi, Johannes Kirchmair
2025	J	`jnl`	NEAT: Neighborhood-Guided, Efficient, Autoregressive Set Transformer for 3D Molecular Generation. CoRR Daniel Rose, Roxane Axel Jacob, Johannes Kirchmair, Thierry Langer
2025	J	`jnl`	Site-of-Metabolism Prediction with Aleatoric and Epistemic Uncertainty Quantification. J. Chem. Inf. Model. Roxane Axel Jacob, Oliver Wieder, Ya Chen, Angelica Mazzolari, Andreas Bergner, Klaus-Jürgen Schleifer, Johannes Kirchmair
2024	J	`jnl`	Active Learning Approach for Guiding Site-of-Metabolism Measurement and Annotation. J. Chem. Inf. Model. Ya Chen, Thomas Seidel, Roxane Axel Jacob, Steffen Hirte, Angelica Mazzolari, Alessandro Pedretti, Giulio Vistoli, Thierry Langer, Filip Miljkovic, Johannes Kirchmair
2024	J	`jnl`	Deciphering Molecular Embeddings with Centered Kernel Alignment. J. Chem. Inf. Model. Matthias Welsch, Steffen Hirte, Johannes Kirchmair
2024	J	`jnl`	Quantifying the Hardness of Bioactivity Prediction Tasks for Transfer Learning. J. Chem. Inf. Model. Hosein Fooladi, Steffen Hirte, Johannes Kirchmair
2023	J	`jnl`	DNN-PP: A novel Deep Neural Network approach and its applicability in drug-related property prediction. Expert Syst. Appl. Magdalena Wiercioch, Johannes Kirchmair
2023	J	`jnl`	School of cheminformatics in Latin America. J. Cheminformatics 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
2021	J	`jnl`	ChemBioSim: Enhancing Conformal Prediction of In Vivo Toxicity by Use of Predicted Bioactivities. J. Chem. Inf. Model. Marina Garcia de Lomana, Andrea Morger, Ulf Norinder, Roland Buesen, Robert Landsiedel, Andrea Volkamer, Johannes Kirchmair, Miriam Mathea
2021	J	`jnl`	Computational Applications in Secondary Metabolite Discovery (CAiSMD): an online workshop. J. Cheminformatics 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
2021	J	`jnl`	Rationality over fashion and hype in drug design. F1000Research José L. Medina-Franco, Karina Martínez-Mayorga, Eli Fernández-de Gortari, Johannes Kirchmair, Jürgen Bajorath
2020	J	`jnl`	NERDD: a web portal providing access to in silico tools for drug discovery. Bioinform. Conrad Stork, Gerd Embruch, Martin Sícho, Christina de Bruyn Kops, Ya Chen, Daniel Svozil, Johannes Kirchmair
2020	J	`jnl`	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. Ya Chen, Neann Mathai, Johannes Kirchmair
2020	J	`jnl`	Validation strategies for target prediction methods. Briefings Bioinform. Neann Mathai, Ya Chen, Johannes Kirchmair
2019	J	`jnl`	Conformator: A Novel Method for the Generation of Conformer Ensembles. J. Chem. Inf. Model. Nils-Ole Friedrich, Florian Flachsenberg, Agnes Meyder, Kai Sommer, Johannes Kirchmair, Matthias Rarey
2019	J	`jnl`	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. Martin Sícho, Conrad Stork, Angelica Mazzolari, Christina de Bruyn Kops, Alessandro Pedretti, Bernard Testa, Giulio Vistoli, Daniel Svozil, Johannes Kirchmair
2019	J	`jnl`	Hit Dexter 2.0: Machine-Learning Models for the Prediction of Frequent Hitters. J. Chem. Inf. Model. Conrad Stork, Ya Chen, Martin Sícho, Johannes Kirchmair
2018	J	`jnl`	Characterization of the Chemical Space of Known and Readily Obtainable Natural Products. J. Chem. Inf. Model. Ya Chen, Marina Garcia de Lomana, Nils-Ole Friedrich, Johannes Kirchmair
2017	J	`jnl`	Alignment-Based Prediction of Sites of Metabolism. J. Chem. Inf. Model. Christina de Bruyn Kops, Nils-Ole Friedrich, Johannes Kirchmair
2017	J	`jnl`	Benchmarking Commercial Conformer Ensemble Generators. J. Chem. Inf. Model. Nils-Ole Friedrich, Christina de Bruyn Kops, Florian Flachsenberg, Kai Sommer, Matthias Rarey, Johannes Kirchmair
2017	J	`jnl`	Data Resources for the Computer-Guided Discovery of Bioactive Natural Products. J. Chem. Inf. Model. Ya Chen, Christina de Bruyn Kops, Johannes Kirchmair
2017	J	`jnl`	FAME 2: Simple and Effective Machine Learning Model of Cytochrome P450 Regioselectivity. J. Chem. Inf. Model. Martin Sícho, Christina de Bruyn Kops, Conrad Stork, Daniel Svozil, Johannes Kirchmair
2017	J	`jnl`	High-Quality Dataset of Protein-Bound Ligand Conformations and Its Application to Benchmarking Conformer Ensemble Generators. J. Chem. Inf. Model. Nils-Ole Friedrich, Agnes Meyder, Christina de Bruyn Kops, Kai Sommer, Florian Flachsenberg, Matthias Rarey, Johannes Kirchmair
2014	J	`jnl`	Cytochrome P450 site of metabolism prediction from 2D topological fingerprints using GPU accelerated probabilistic classifiers. J. Cheminformatics Jonathan D. Tyzack, Hamse Y. Mussa, Mark J. Williamson, Johannes Kirchmair, Robert C. Glen
2013	J	`jnl`	FAst MEtabolizer (FAME): A Rapid and Accurate Predictor of Sites of Metabolism in Multiple Species by Endogenous Enzymes. J. Chem. Inf. Model. Johannes Kirchmair, Mark J. Williamson, Avid M. Afzal, Jonathan D. Tyzack, Alison P. K. Choy, Andrew Howlett, Patrik Rydberg, Robert C. Glen
2013	J	`jnl`	How Do Metabolites Differ from Their Parent Molecules and How Are They Excreted? J. Chem. Inf. Model. 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
2013	J	`jnl`	Quantifying the shifts in physicochemical property space introduced by the metabolism of small organic molecules. J. Cheminformatics 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
2012	J	`jnl`	Computational Prediction of Metabolism: Sites, Products, SAR, P450 Enzyme Dynamics, and Mechanisms. J. Chem. Inf. Model. Johannes Kirchmair, Mark J. Williamson, Jonathan D. Tyzack, Lu Tan, Peter J. Bond, Andreas Bender, Robert C. Glen
2010	J	`jnl`	One Concept, Three Implementations of 3D Pharmacophore-Based Virtual Screening: Distinct Coverage of Chemical Search Space. J. Chem. Inf. Model. Gudrun M. Spitzer, Mathias Heiss, Martina Mangold, Patrick Markt, Johannes Kirchmair, Gerhard Wolber, Klaus R. Liedl
2009	J	`jnl`	Critical Comparison of Virtual Screening Methods against the MUV Data Set. J. Chem. Inf. Model. Pekka Tiikkainen, Patrick Markt, Gerhard Wolber, Johannes Kirchmair, Simona Distinto, Antti Poso, Olli-P. Kallioniemi
2009	J	`jnl`	How To Optimize Shape-Based Virtual Screening: Choosing the Right Query and Including Chemical Information. J. Chem. Inf. Model. Johannes Kirchmair, Simona Distinto, Patrick Markt, Daniela Schuster, Gudrun M. Spitzer, Klaus R. Liedl, Gerhard Wolber
2009	J	`jnl`	Hydrogen-Bonding Patterns of Minor Groove-Binder-DNA Complexes Reveal Criteria for Discovery of New Scaffolds. J. Chem. Inf. Model. Gudrun M. Spitzer, Bernd Wellenzohn, Patrick Markt, Johannes Kirchmair, Thierry Langer, Klaus R. Liedl
2008	J	`jnl`	Discovery of Novel Cathepsin S Inhibitors by Pharmacophore-Based Virtual High-Throughput Screening. J. Chem. Inf. Model. 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
2008	J	`jnl`	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. Johannes Kirchmair, Patrick Markt, Simona Distinto, Gerhard Wolber, Thierry Langer
2007	J	`jnl`	CAESAR: A New Conformer Generation Algorithm Based on Recursive Buildup and Local Rotational Symmetry Consideration. J. Chem. Inf. Model. Jiabo Li, Tedman Ehlers, Jon M. Sutter, Shikha Varma-O'Brien, Johannes Kirchmair
2007	J	`jnl`	Fast and Efficient in Silico 3D Screening: Toward Maximum Computational Efficiency of Pharmacophore-Based and Shape-Based Approaches. J. Chem. Inf. Model. Johannes Kirchmair, Stojanka Ristic, Kathrin Eder, Patrick Markt, Gerhard Wolber, Christian Laggner, Thierry Langer
2007	J	`jnl`	Pharmacophore modeling and parallel screening for PPAR ligands. J. Comput. Aided Mol. Des. Patrick Markt, Daniela Schuster, Johannes Kirchmair, Christian Laggner, Thierry Langer
2006	J	`jnl`	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. Johannes Kirchmair, Gerhard Wolber, Christian Laggner, Thierry Langer
2005	J	`jnl`	Comparative Analysis of Protein-Bound Ligand Conformations with Respect to Catalyst's Conformational Space Subsampling Algorithms. J. Chem. Inf. Model. Johannes Kirchmair, Christian Laggner, Gerhard Wolber, Thierry Langer