Evaluation of extended parameter sets for the 3D-QSAR technique MaP: Implications for interpretability and model quality exemplified by antimalarially active naphthylisoquinoline alkaloids. - Nikolaus Stiefl; Gerhard Bringmann; Christian Rummey; Knut Baumann (J. Comput. Aided Mol. Des., 2003)

Validation tools for variable subset regression. - Knut Baumann; Nikolaus Stiefl (J. Comput. Aided Mol. Des., 2004)

Structure-Based Validation of the 3D-QSAR Technique MaP. - Nikolaus Stiefl; Knut Baumann (J. Chem. Inf. Model., 2005)

ErG: 2D Pharmacophore Descriptions for Scaffold Hopping. - Nikolaus Stiefl; Ian A. Watson; Knut Baumann; Andrea Zaliani (J. Chem. Inf. Model., 2006)

A Knowledge-Based Weighting Approach to Ligand-Based Virtual Screening. - Nikolaus Stiefl; Andrea Zaliani (J. Chem. Inf. Model., 2006)

Evaluation of machine-learning methods for ligand-based virtual screening. - Beining Chen; Robert F. Harrison; George Papadatos; Peter Willett 002; David J. Wood; Xiao Qing Lewell; Paulette A. Greenidge; Nikolaus Stiefl (J. Comput. Aided Mol. Des., 2007)

Making sure there's a "give" associated with the "take": producing and using open-source software in big pharma. - Gregory A. Landrum; Richard A. Lewis; Andrew Palmer; Nikolaus Stiefl; Anna Vulpetti (J. Cheminformatics, 2011)

Bringing the MMFF force field to the RDKit: implementation and validation. - Paolo Tosco; Nikolaus Stiefl; Gregory A. Landrum (J. Cheminformatics, 2014)

The integration of Open3DTOOLS into the RDKit and KNIME. - Paolo Tosco; Nikolaus Stiefl; Gregory A. Landrum (J. Cheminformatics, 2014)

FOCUS - Development of a Global Communication and Modeling Platform for Applied and Computational Medicinal Chemists. - Nikolaus Stiefl; Peter Gedeck; Donovan Chin; Peter Hunt; Mika K. Lindvall; Katrin Spiegel; Clayton Springer; Scott Biller; Christoph L. Buenemann; Takanori Kanazawa; Mitsunori Kato; Richard A. Lewis; et al. (J. Chem. Inf. Model., 2015)

What's What: The (Nearly) Definitive Guide to Reaction Role Assignment. - Nadine Schneider; Nikolaus Stiefl; Gregory A. Landrum (J. Chem. Inf. Model., 2016)

Chemical Topic Modeling: Exploring Molecular Data Sets Using a Common Text-Mining Approach. - Nadine Schneider; Nikolas Fechner; Gregory A. Landrum; Nikolaus Stiefl (J. Chem. Inf. Model., 2017)

xMaP - An Interpretable Alignment-Free Four-Dimensional Quantitative Structure-Activity Relationship Technique Based on Molecular Surface Properties and Conformer Ensembles. - Jan Dreher; Josef Scheiber; Nikolaus Stiefl; Knut Baumann (J. Chem. Inf. Model., 2018)

Drug Analogs from Fragment-Based Long Short-Term Memory Generative Neural Networks. - Mahendra Awale; Finton Sirockin; Nikolaus Stiefl; Jean-Louis Reymond (J. Chem. Inf. Model., 2019)

Automated Identification of Chemical Series: Classifying like a Medicinal Chemist. - Franziska Kruger; Nikolas Fechner; Nikolaus Stiefl (J. Chem. Inf. Model., 2020)

rdScaffoldNetwork: The Scaffold Network Implementation in RDKit. - Franziska Kruger; Nikolaus Stiefl; Gregory A. Landrum (J. Chem. Inf. Model., 2020)

Ten simple rules to power drug discovery with data science. - Enrico Ferrero; Sophie Brachat; Jeremy L. Jenkins; Philippe Marc; Peter Skewes-Cox; Robert C. Altshuler; Caroline Gubser Keller; Audrey Kauffmann; Erik K. Sassaman; Jason M. Laramie; Birgit Schoeberl; Mark L. Borowsky; et al. (PLoS Comput. Biol., 2020)

Learning to Extend Molecular Scaffolds with Structural Motifs. - Krzysztof Maziarz; Henry Jackson-Flux; Pashmina Cameron; Finton Sirockin; Nadine Schneider; Nikolaus Stiefl; Marc Brockschmidt (CoRR, 2021)

GHOST: Adjusting the Decision Threshold to Handle Imbalanced Data in Machine Learning. - Carmen Esposito; Gregory A. Landrum; Nadine Schneider; Nikolaus Stiefl; Sereina Riniker (J. Chem. Inf. Model., 2021)

Learning to Extend Molecular Scaffolds with Structural Motifs. - Krzysztof Maziarz; Henry Richard Jackson-Flux; Pashmina Cameron; Finton Sirockin; Nadine Schneider; Nikolaus Stiefl; Marwin H. S. Segler; Marc Brockschmidt (ICLR, 2022)

25 Years of Small-Molecule Optimization at Novartis: A Retrospective Analysis of Chemical Series Evolution. - Maximilian Beckers; Nikolas Fechner; Nikolaus Stiefl (J. Chem. Inf. Model., 2022)

PREFER: A New Predictive Modeling Framework for Molecular Discovery. - Jessica Lanini; Gianluca Santarossa; Finton Sirockin; Richard A. Lewis; Nikolas Fechner; Hubert Misztela; Sarah Lewis; Krzysztof Maziarz; Megan Stanley; Marwin H. S. Segler; Nikolaus Stiefl; Nadine Schneider (J. Chem. Inf. Model., 2023)

SIMPD: an algorithm for generating simulated time splits for validating machine learning approaches. - Gregory A. Landrum; Maximilian Beckers; Jessica Lanini; Nadine Schneider; Nikolaus Stiefl; Sereina Riniker (J. Cheminformatics, 2023)

Balancing Molecular Size, Activity, Permeability, and Other Properties: Drug Candidates in the Context of Their Chemical Structure Optimization. - Maximilian Beckers; Finton Sirockin; Nikolas Fechner; Nikolaus Stiefl (J. Chem. Inf. Model., 2024)