Publications

Fabian Liessmann, Lukas von Bredow, Jens Meiler, und rahm Liebscher, Ines. Targeting adhesion G protein-coupled receptors. Current status and future perspectives. Structure, Elsevier, November 2024. [PUMA: topic_lifescience ADGRG1; ADGRG2; ADGRG3; ADGRG5; ADGRG6; ADGRG7; GPCRs; GPR114; GPR126; GPR128; GPR56; GPR64; GPR97; adhesion area_bigdata discovery; drug ep ligands; molecules; small structure]

Nadja Meumann, Marti Cabanes-Creus, Moritz Ertelt, Renina Gale Navarro, Julie Lucifora, Qinggong Yuan, Karin Nien-Huber, Ahmed Abdelrahman, Xuan-Khang Vu, Liang Zhang, und others. Adeno-associated virus serotype 2 capsid variants for improved liver-directed gene therapy. Hepatology, (77)3:802--815, LWW, 2023. [PUMA: topic_lifescience imported]

Laura M. Chamness, Charles P. Kuntz, Andrew G. McKee, Wesley D. Penn, Christopher M. Hemmerich, Douglas B. Rusch, Hope Woods, Dyotima, Jens Meiler, und Jonathan P. Schlebach. Divergent Pairwise Epistasis in the Context of Unstable Membrane Protein Variants. eLife Sciences Publications, Ltd, Dezember 2023. [PUMA: topic_lifescience imported] 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: topic_lifescience imported] URL

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

Davide Sala, Peter W. Hildebrand, und Jens Meiler. Biasing AlphaFold2 to predict GPCRs and kinases with user-defined functional or structural properties. Frontiers in Molecular Biosciences, (10)Frontiers Media SA, Februar 2023. [PUMA: topic_lifescience imported] URL

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

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

Benjamin P. Brown, Richard A. Stein, Jens Meiler, und Hassane Mchaourab. Approximating conformational Boltzmann distributions with AlphaFold2 predictions. Cold Spring Harbor Laboratory, August 2023. [PUMA: topic_lifescience imported] 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 assembly by AlphaFold2. Biophysical Journal, (122)11:2041–2052, Elsevier BV, Juni 2023. [PUMA: topic_lifescience imported] 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: topic_lifescience imported] URL

Alican Gulsevin, und Jens Meiler. Benchmarking Peptide Structure Prediction with AlphaFold2. Cold Spring Harbor Laboratory, Februar 2022. [PUMA: topic_lifescience imported] 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: topic_lifescience imported] 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, und Fyodor A Kondrashov. Heterogeneity of the GFP fitness landscape and data-driven protein design. eLife, (11)eLife Sciences Publications, Ltd, Mai 2022. [PUMA: topic_lifescience imported] URL

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

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: topic_lifescience imported] 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: topic_lifescience imported] URL

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

Benjamin P. Brown, Richard A. Stein, Jens Meiler, und Hassane S. Mchaourab. Approximating Projections of Conformational Boltzmann Distributions with AlphaFold2 Predictions: Opportunities and Limitations. Journal of Chemical Theory and Computation, (20)3:1434–1447, American Chemical Society (ACS), Januar 2024. [PUMA: topic_lifescience imported] URL

Eli Fritz McDonald, Kathryn E. Oliver, Jonathan P. Schlebach, Jens Meiler, und Lars Plate. Benchmarking AlphaMissense pathogenicity predictions against cystic fibrosis variants. In Jeffrey L Brodsky (Hrsg.), PLOS ONE, (19)1:e0297560, Public Library of Science (PLoS), Januar 2024. [PUMA: topic_lifescience imported] 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: topic_lifescience imported] 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: topic_lifescience imported] URL

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

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

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

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

Saksham Phul, Georg Kuenze, Carlos G. Vanoye, Charles R. Sanders, Alfred L. George, und Jens Meiler. Predicting the Functional Impact of KCNQ1 Variants with Artificial Neural Networks. Cold Spring Harbor Laboratory, Dezember 2021. [PUMA: imported topic_lifescience] URL

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

Sandeepkumar Kothiwale, Corina Borza, Ambra Pozzi, und 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, und 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), Oktober 2001. [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, und Fyodor A. Kondrashov. Heterogeneity of the GFP fitness landscape and data-driven protein design. Cold Spring Harbor Laboratory, Dezember 2021. [PUMA: imported topic_lifescience] URL

Jens Meiler, und 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, Oktober 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, und 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, und Jens Meiler. Sampling the conformational landscapes of transporters and receptors with AlphaFold2. Cold Spring Harbor Laboratory, November 2021. [PUMA: imported topic_lifescience] URL

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

Oanh Vu, Jeffrey Mendenhall, Doaa Altarawy, und 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, und 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, und 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, Februar 2016. [PUMA: imported topic_lifescience] URL

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

Benjamin P. Brown, Jeffrey Mendenhall, Alexander R. Geanes, und 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), Januar 2021. [PUMA: imported topic_lifescience] URL

Mariusz Butkiewicz, Ralf Mueller, Danilo Selic, Eric Dawson, und 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, März 2009. [PUMA: imported topic_lifescience] URL