Publications

Minh H Tran, Clara T Schoeder, Kevin L Schey, und Jens Meiler. Computational structure prediction for antibody-antigen complexes from hydrogen-deuterium exchange mass spectrometry: Challenges and outlook. Front. Immunol., (13):859964, Frontiers Media SA, Mai 2022. [PUMA: topic_lifescience (HDX-MS); antibody-antigen biology; docking; epitope-paratope exchange hydrogen-deuterium identification; integrative interaction; mass modeling protein-protein spectrometry structural structure]

Davide Sala, Diego Del Alamo, Hassane S Mchaourab, und Jens Meiler. Modeling of protein conformational changes with Rosetta guided by limited experimental data. Structure, (30)8:1157--1168.e3, Elsevier BV, August 2022. [PUMA: topic_lifescience EPR Rosetta; biology; changes; conformational dynamics; integrative modeling; molecular protein refinement spectroscopy; structural structure]

Bian Li, Jeffrey Mendenhall, John A Capra, und Jens Meiler. A multitask deep-learning method for predicting membrane associations and secondary structures of proteins. J. Proteome Res., (20)8:4089--4100, American Chemical Society (ACS), August 2021. [PUMA: convolutional deep learning; long memory multitask networks; neural prediction prediction; secondary short-term structure topic_lifescience topology transmembrane]

Pranav Kodali, Clara T Schoeder, Samuel Schmitz, James E Crowe, Jr, und Jens Meiler. RosettaCM for antibodies with very long HCDR3s and low template availability. Proteins, (89)11:1458--1472, Wiley, November 2021. [PUMA: Rosetta; antibody; benchmark; homology loop modeling; prediction; structure topic_lifescience]

Ronny Lorenz, und Peter F Stadler. RNA secondary structures with limited base pair span: Exact backtracking and an application. Genes (Basel), (12)1:14, MDPI AG, Dezember 2020. [PUMA: RNA algorithm elements; hyper-stable prediction; scanning secondary structure]

Davide Sala, Peter W Hildebrand, und Jens Meiler. Biasing AlphaFold2 to predict GPCRs and kinases with user-defined functional or structural properties. Front. Mol. Biosci., (10):1121962, Februar 2023. [PUMA: topic_lifescience (G-protein-coupled AlphaFold; GPCRs function; kinases; prediction protein receptors); structure]

Kaitlyn V Ledwitch, Georg Künze, Jacob R McKinney, Elleansar Okwei, Katherine Larochelle, Lisa Pankewitz, Soumya Ganguly, Heather L Darling, Irene Coin, und Jens Meiler. Sparse pseudocontact shift NMR data obtained from a non-canonical amino acid-linked lanthanide tag improves integral membrane protein structure prediction. J. Biomol. NMR, (77)3:69--82, Juni 2023. [PUMA: topic_lifescience (IMPs); (PCSs); (ncAAs); Click Integral Non-canonical Pseudocontact Rosetta; Structure acids amino chemistry; membrane prediction proteins shifts]