Johannes Kirchmair

Publication Activity (10 Years)

Years Active: 2005-2024
Publications (10 Years): 19

Top Topics

Probabilistic Classifiers

Conformal Prediction

Top Venues

J. Chem. Inf. Model.

J. Cheminformatics

Briefings Bioinform.

Publications

Hosein Fooladi, Steffen Hirte, Johannes Kirchmair
Quantifying the Hardness of Bioactivity Prediction Tasks for Transfer Learning. J. Chem. Inf. Model. 64 (10) (2024)
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) (2024)
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) (2023)
Karla Gonzalez-Ponce, Carolina Horta Andrade, Fiona 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) (2023)
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 (2021)
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) (2021)
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) (2021)
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) (2020)
Neann Mathai, Ya Chen, Johannes Kirchmair
Validation strategies for target prediction methods. Briefings Bioinform. 21 (3) (2020)
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) (2020)
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) (2019)
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) (2019)
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) (2019)
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) (2018)
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) (2017)
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) (2017)
Christina de Bruyn Kops, Nils-Ole Friedrich, Johannes Kirchmair
Alignment-Based Prediction of Sites of Metabolism. J. Chem. Inf. Model. 57 (6) (2017)
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) (2017)
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) (2017)
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) (2014)
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) (2013)
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) (2013)
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) (2013)
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) (2012)
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) (2010)
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) (2009)
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) (2009)
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) (2009)
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) (2008)
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) (2008)
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) (2007)
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) (2007)
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) (2007)
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) (2006)
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) (2005)