Publications

Yunchao (Lance) Liu, Yu Wang, Oanh Vu, Rocco Moretti, Bobby Bodenheimer, Jens Meiler, and 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), June 2023. [PUMA: imported topic_lifescience] URL

D. Sala, F. Engelberger, H.S. Mchaourab, and 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, and Lars Plate. Benchmarking AlphaMissense Pathogenicity Predictions Against Cystic Fibrosis Variants. Cold Spring Harbor Laboratory, October 2023. [PUMA: imported topic_lifescience] URL

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

Moritz Ertelt, Rocco Moretti, Jens Meiler, and 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, June 2024. [PUMA: imported topic_lifescience] URL

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

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

Bian Li, Jeffrey Mendenhall, John A. Capra, and 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), July 2021. [PUMA: imported topic_lifescience] URL

Gregory Sliwoski, Jeffrey Mendenhall, and 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, December 2015. [PUMA: imported topic_lifescience] URL

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

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

Yunchao (Lance) Liu, Rocco Moretti, Yu Wang, Ha Dong, Bailu Yan, Bobby Bodenheimer, Tyler Derr, and 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, and 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, and 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, and Edward W. Lowe. Computational Methods in Drug Discovery. In Eric L. Barker (Eds.), Pharmacological Reviews, (66)1:334–395, American Society for Pharmacology & Experimental Therapeutics (ASPET), December 2013. [PUMA: imported topic_lifescience] URL

Gregory Sliwoski, Edward W. Lowe, Mariusz Butkiewicz, and 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, and Jens Meiler. Benchmarking Peptide Structure Prediction with AlphaFold2. Cold Spring Harbor Laboratory, February 2022. [PUMA: imported topic_lifescience] URL

Shan Jiang, Zhaoqian Su, Nathaniel Bloodworth, Yunchao Liu, Cristina Martina, David G. Harrison, and 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, and 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, February 2022. [PUMA: imported topic_lifescience] URL

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