Publications

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