Publications

Yunchao (Lance) Liu, Yu Wang, Oanh Vu, Rocco Moretti, Bobby Bodenheimer, Jens Meiler, und Tyler Derr. Interpretable Chirality-Aware Graph Neural Network for Quantitative Structure Activity Relationship Modeling in Drug Discovery. Proceedings of the AAAI Conference on Artificial Intelligence, (37)12:14356–14364, Association for the Advancement of Artificial Intelligence (AAAI), Juni 2023. [PUMA: imported topic_lifescience] URL

D. Sala, F. Engelberger, H.S. Mchaourab, und J. Meiler. Modeling conformational states of proteins with AlphaFold. Current Opinion in Structural Biology, (81):102645, Elsevier BV, August 2023. [PUMA: imported topic_lifescience] URL

Eli Fritz McDonald, Kathryn E. Oliver, Jonathan P. Schlebach, Jens Meiler, und Lars Plate. Benchmarking AlphaMissense Pathogenicity Predictions Against Cystic Fibrosis Variants. Cold Spring Harbor Laboratory, Oktober 2023. [PUMA: imported topic_lifescience] URL

Moritz Ertelt, Vikram Khipple Mulligan, Jack B. Maguire, Sergey Lyskov, Rocco Moretti, Torben Schiffner, Jens Meiler, und Clara T. Schoeder. Combining machine learning with structure-based protein design to predict and engineer post-translational modifications of proteins. In Joanna Slusky (Hrsg.), PLOS Computational Biology, (20)3:e1011939, Public Library of Science (PLoS), März 2024. [PUMA: imported topic_lifescience] URL

Moritz Ertelt, Rocco Moretti, Jens Meiler, und Clara T. Schoeder. Self-supervised machine learning methods for protein design improve sampling, but not the identification of high-fitness variants. Cold Spring Harbor Laboratory, Juni 2024. [PUMA: imported topic_lifescience] URL

Alican Gulsevin, Bing Han, Jason C. Porta, Hassane S. Mchaourab, Jens Meiler, und Anne K. Kenworthy. Template-free prediction of a new monotopic membrane protein fold and oligomeric assembly by Alphafold2. Cold Spring Harbor Laboratory, Juli 2022. [PUMA: imported topic_lifescience] URL

Diego del Alamo, Davide Sala, Hassane S Mchaourab, und Jens Meiler. Sampling alternative conformational states of transporters and receptors with AlphaFold2. eLife, (11)eLife Sciences Publications, Ltd, März 2022. [PUMA: imported topic_lifescience] URL

Bian Li, Jeffrey Mendenhall, John A. Capra, und Jens Meiler. A Multitask Deep-Learning Method for Predicting Membrane Associations and Secondary Structures of Proteins. Journal of Proteome Research, (20)8:4089–4100, American Chemical Society (ACS), Juli 2021. [PUMA: imported topic_lifescience] URL

Gregory Sliwoski, Jeffrey Mendenhall, und Jens Meiler. Autocorrelation descriptor improvements for QSAR: 2DA_Sign and 3DA_Sign. Journal of Computer-Aided Molecular Design, (30)3:209–217, Springer Science and Business Media LLC, Dezember 2015. [PUMA: imported topic_lifescience] URL

Michael Kuhn, Jens Meiler, und David Baker. Strand‐loop‐strand motifs: Prediction of hairpins and diverging turns in proteins. Proteins: Structure, Function, and Bioinformatics, (54)2:282–288, Wiley, Dezember 2003. [PUMA: imported topic_lifescience] URL

Charles P. Kuntz, Hope Woods, Andrew G. McKee, Nathan B. Zelt, Jeffrey L. Mendenhall, Jens Meiler, und Jonathan P. Schlebach. Towards Generalizable Predictions for the Effects of Mutations on G-Protein Coupled Receptor Expression. Cold Spring Harbor Laboratory, Dezember 2021. [PUMA: imported topic_lifescience] URL

Yunchao (Lance) Liu, Rocco Moretti, Yu Wang, Ha Dong, Bailu Yan, Bobby Bodenheimer, Tyler Derr, und Jens Meiler. Advancements in Ligand-Based Virtual Screening through the Synergistic Integration of Graph Neural Networks and Expert-Crafted Descriptors. Cold Spring Harbor Laboratory, April 2023. [PUMA: imported topic_lifescience] URL

Jens Meiler, Walter Maier, Martin Will, und Reinhard Meusinger. Using Neural Networks for 13C NMR Chemical Shift Prediction–Comparison with Traditional Methods. Journal of Magnetic Resonance, (157)2:242–252, Elsevier BV, August 2002. [PUMA: imported topic_lifescience] URL

Vladimir Golkov, Marcin J. Skwark, Atanas Mirchev, Georgi Dikov, Alexander R. Geanes, Jeffrey Mendenhall, Jens Meiler, und Daniel Cremers. 3D Deep Learning for Biological Function Prediction from Physical Fields. 2020 International Conference on 3D Vision (3DV), 928–937, IEEE, November 2020. [PUMA: imported topic_lifescience] URL

Gregory Sliwoski, Sandeepkumar Kothiwale, Jens Meiler, und Edward W. Lowe. Computational Methods in Drug Discovery. In Eric L. Barker (Hrsg.), Pharmacological Reviews, (66)1:334–395, American Society for Pharmacology & Experimental Therapeutics (ASPET), Dezember 2013. [PUMA: imported topic_lifescience] URL

Gregory Sliwoski, Edward W. Lowe, Mariusz Butkiewicz, und Jens Meiler. BCL::EMAS — Enantioselective Molecular Asymmetry Descriptor for 3D-QSAR. Molecules, (17)8:9971–9989, MDPI AG, August 2012. [PUMA: imported topic_lifescience] URL

Alican Gulsevin, und Jens Meiler. Benchmarking Peptide Structure Prediction with AlphaFold2. Cold Spring Harbor Laboratory, Februar 2022. [PUMA: imported topic_lifescience] URL

Shan Jiang, Zhaoqian Su, Nathaniel Bloodworth, Yunchao Liu, Cristina Martina, David G. Harrison, und Jens Meiler. Machine learning application to predict binding affinity between peptide containing non-canonical amino acids and HLA0201. Cold Spring Harbor Laboratory, November 2024. [PUMA: imported topic_lifescience] URL

Benjamin P. Brown, Oanh Vu, Alexander R. Geanes, Sandeepkumar Kothiwale, Mariusz Butkiewicz, Edward W. Lowe, Ralf Mueller, Richard Pape, Jeffrey Mendenhall, und Jens Meiler. Introduction to the BioChemical Library (BCL): An Application-Based Open-Source Toolkit for Integrated Cheminformatics and Machine Learning in Computer-Aided Drug Discovery. Frontiers in Pharmacology, (13)Frontiers Media SA, Februar 2022. [PUMA: imported topic_lifescience] URL

Sam DeLuca, und Jens Meiler. A Novel Method for Guiding Protein-Ligand Docking with QSAR-Derived Pharmacophore Maps. Biophysical Journal, (100)3:394a–395a, Elsevier BV, Februar 2011. [PUMA: imported topic_lifescience] URL