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

Saksham Phul, Georg Kuenze, Carlos G. Vanoye, Charles R. Sanders, Alfred L. George, and Jens Meiler. Predicting the Functional Impact of KCNQ1 Variants with Artificial Neural Networks. Cold Spring Harbor Laboratory, December 2021. [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. In Jeffrey L Brodsky (Eds.), PLOS ONE, (19)1:e0297560, Public Library of Science (PLoS), January 2024. [PUMA: imported topic_lifescience] URL

Marion F. S. Fischer, James E. Crowe, and Jens Meiler. Computational epitope mapping of class I fusion proteins using low complexity supervised learning methods. In Dina Schneidman (Eds.), PLOS Computational Biology, (18)12:e1010230, Public Library of Science (PLoS), December 2022. [PUMA: imported topic_lifescience] URL

Vladimir Golkov, Alexander Becker, Daniel T. Plop, Daniel Čuturilo, Neda Davoudi, Jeffrey Mendenhall, Rocco Moretti, Jens Meiler, and Daniel Cremers. Deep Learning for Virtual Screening: Five Reasons to Use ROC Cost Functions. arXiv, 2020. [PUMA: imported topic_lifescience] URL

Xiaohan Kuang, zhaoqian su, Yunchao Liu, Xiaobo Lin, Jesse Spencer Smith, Tyler Derr, Yinghao Wu, and Jens Meiler. SuperWater: Predicting Water Molecule Positions on Protein Structures by Generative AI. Cold Spring Harbor Laboratory, November 2024. [PUMA: imported topic_lifescience] URL

Sandeepkumar Kothiwale, Corina Borza, Ambra Pozzi, and Jens Meiler. Quantitative Structure–Activity Relationship Modeling of Kinase Selectivity Profiles. Molecules, (22)9:1576, MDPI AG, September 2017. [PUMA: imported topic_lifescience] URL

Jens Meiler, and Martin Will. Automated Structure Elucidation of Organic Molecules from 13C NMR Spectra Using Genetic Algorithms and Neural Networks. Journal of Chemical Information and Computer Sciences, (41)6:1535–1546, American Chemical Society (ACS), October 2001. [PUMA: imported topic_lifescience] URL

Alexandra M. Blee, Bian Li, Turner Pecen, Jens Meiler, Zachary D. Nagel, John A. Capra, and Walter J. Chazin. An Active Learning Framework Improves Tumor Variant Interpretation. Cancer Research, (82)15:2704–2715, American Association for Cancer Research (AACR), June 2022. [PUMA: imported topic_lifescience] URL

Louisa Gonzalez Somermeyer, Aubin Fleiss, Alexander S. Mishin, Nina G. Bozhanova, Anna A. Igolkina, Jens Meiler, Maria-Elisenda Alaball Pujol, Ekaterina V. Putintseva, Karen S. Sarkisyan, and Fyodor A. Kondrashov. Heterogeneity of the GFP fitness landscape and data-driven protein design. Cold Spring Harbor Laboratory, December 2021. [PUMA: imported topic_lifescience] URL

Jens Meiler, and David Baker. Coupled prediction of protein secondary and tertiary structure. Proceedings of the National Academy of Sciences, (100)21:12105–12110, Proceedings of the National Academy of Sciences, October 2003. [PUMA: imported topic_lifescience] URL

Alexander R. Geanes, Hykeyung P. Cho, Kellie D. Nance, Kevin M. McGowan, P. Jeffrey Conn, Carrie K. Jones, Jens Meiler, and Craig W. Lindsley. Ligand-based virtual screen for the discovery of novel M5 inhibitor chemotypes. Bioorganic & Medicinal Chemistry Letters, (26)18:4487–4491, Elsevier BV, September 2016. [PUMA: imported topic_lifescience] URL

Diego del Alamo, Davide Sala, Hassane S. Mchaourab, and Jens Meiler. Sampling the conformational landscapes of transporters and receptors with AlphaFold2. Cold Spring Harbor Laboratory, November 2021. [PUMA: imported topic_lifescience] URL

Christopher W. Moth, Jonathan H. Sheehan, Abdullah Al Mamun, R. Michael Sivley, Alican Gulsevin, David Rinker, John A. Capra, and Jens Meiler. VUStruct: a compute pipeline for high throughput and personalized structural biology. Cold Spring Harbor Laboratory, August 2024. [PUMA: imported topic_lifescience] URL

Caleb A. H. Jones, Benjamin P. Brown, Daniel C. Schultz, Julie Engers, Valerie M. Kramlinger, Jens Meiler, and Craig W. Lindsley. Computer-Aided Design and Biological Evaluation of Diazaspirocyclic D4R Antagonists. ACS Chemical Neuroscience, (15)12:2396–2407, American Chemical Society (ACS), June 2024. [PUMA: imported topic_lifescience] URL

Julia Koehler, Nils Woetzel, René Staritzbichler, Charles R. Sanders, and Jens Meiler. A unified hydrophobicity scale for multispan membrane proteins. Proteins: Structure, Function, and Bioinformatics, (76)1:13–29, Wiley, December 2008. [PUMA: imported topic_lifescience] URL

Oanh Vu, Jeffrey Mendenhall, Doaa Altarawy, and Jens Meiler. BCL::Mol2D—a robust atom environment descriptor for QSAR modeling and lead optimization. Journal of Computer-Aided Molecular Design, (33)5:477–486, Springer Science and Business Media LLC, April 2019. [PUMA: imported topic_lifescience] URL

Jens Meiler, Reinhard Meusinger, and Martin Will. Neural Network Prediction of 13C NMR Chemical Shifts of Substituted Benzenes. Monatshefte für Chemie / Chemical Monthly, (130)9:1089–1095, Springer Science and Business Media LLC, September 1999. [PUMA: imported topic_lifescience] URL

Jeffrey Mendenhall, and Jens Meiler. Improving quantitative structure–activity relationship models using Artificial Neural Networks trained with dropout. Journal of Computer-Aided Molecular Design, (30)2:177–189, Springer Science and Business Media LLC, February 2016. [PUMA: imported topic_lifescience] URL

Edward W. Lowe, Alysia Ferrebee, Alice L. Rodriguez, P. Jeffrey Conn, and Jens Meiler. 3D-QSAR CoMFA study of benzoxazepine derivatives as mGluR5 positive allosteric modulators. Bioorganic & Medicinal Chemistry Letters, (20)19:5922–5924, Elsevier BV, October 2010. [PUMA: imported topic_lifescience] URL

Louisa Gonzalez Somermeyer, Aubin Fleiss, Alexander S Mishin, Nina G Bozhanova, Anna A Igolkina, Jens Meiler, Maria-Elisenda Alaball Pujol, Ekaterina V Putintseva, Karen S Sarkisyan, and Fyodor A Kondrashov. Heterogeneity of the GFP fitness landscape and data-driven protein design. eLife, (11)eLife Sciences Publications, Ltd, May 2022. [PUMA: imported topic_lifescience] URL

Benjamin P. Brown, Jeffrey Mendenhall, Alexander R. Geanes, and Jens Meiler. General Purpose Structure-Based Drug Discovery Neural Network Score Functions with Human-Interpretable Pharmacophore Maps. Journal of Chemical Information and Modeling, (61)2:603–620, American Chemical Society (ACS), January 2021. [PUMA: imported topic_lifescience] URL

Mariusz Butkiewicz, Ralf Mueller, Danilo Selic, Eric Dawson, and Jens Meiler. Application of machine learning approaches on quantitative structure activity relationships. 2009 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, 255–262, IEEE, March 2009. [PUMA: imported topic_lifescience] URL

E. W. Lowe, M. Butkiewicz, N. Woetzel, and J. Meiler. GPU-accelerated machine learning techniques enable QSAR modeling of large HTS data. 2012 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), 314–320, IEEE, May 2012. [PUMA: imported topic_lifescience] URL

Mariusz Butkiewicz, Edward W. Lowe, and Jens Meiler. Bcl∷ChemInfo - Qualitative analysis of machine learning models for activation of HSD involved in Alzheimer’s Disease. 2012 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), 329–334, IEEE, May 2012. [PUMA: imported topic_lifescience] URL

Joseph DeCorte, Benjamin Brown, and Jens Meiler. Interpretable deep-learning pKa prediction for small molecule drugs via atomic sensitivity analysis. American Chemical Society (ACS), June 2024. [PUMA: imported topic_lifescience] URL

J. Meiler, R. Meusinger, and M. Will. Fast Determination of 13C NMR Chemical Shifts Using Artificial Neural Networks. Journal of Chemical Information and Computer Sciences, (40)5:1169–1176, American Chemical Society (ACS), August 2000. [PUMA: imported topic_lifescience] URL

Saksham Phul, Georg Kuenze, Carlos G. Vanoye, Charles R. Sanders, Alfred L. George, and Jens Meiler. Predicting the functional impact of KCNQ1 variants with artificial neural networks. In Joanna Slusky (Eds.), PLOS Computational Biology, (18)4:e1010038, Public Library of Science (PLoS), April 2022. [PUMA: imported topic_lifescience] URL

Annalen Bleckmann, and Jens Meiler. Epothilones: Quantitative Structure Activity Relations Studied by Support Vector Machines and Artificial Neural Networks. QSAR & Combinatorial Science, (22)7:722–728, Wiley, October 2003. [PUMA: imported topic_lifescience] URL

Laura M. Chamness, Charles P. Kuntz, Andrew G. McKee, Wesley D. Penn, Christopher M. Hemmerich, Douglas B. Rusch, Hope Woods, Dyotima, Jens Meiler, and Jonathan P. Schlebach. Divergent Pairwise Epistasis in the Context of Unstable Membrane Protein Variants. eLife Sciences Publications, Ltd, December 2023. [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 assembly by AlphaFold2. Biophysical Journal, (122)11:2041–2052, Elsevier BV, June 2023. [PUMA: imported topic_lifescience] URL