Are the chemical families still there? Formal structure of similarity of elements and its thermochemical domain. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, (480)2298The Royal Society, September 2024. [PUMA: Formal chemical families similarity structure zno] URL
Accuracy of RNA Structure Prediction Depends on the Pseudoknot Grammar. Advances in Bioinformatics and Computational Biology, 20–31, Springer Nature Switzerland, 2022. [PUMA: DependsPseudoknot Grammar Prediction RNA Structure] URL
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]
Computational structure prediction for antibody-antigen complexes from hydrogen-deuterium exchange mass spectrometry: Challenges and outlook. Front. Immunol., (13):859964, Frontiers Media SA, May 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]
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]
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]
RNA secondary structures with limited base pair span: Exact backtracking and an application. Genes (Basel), (12)1:14, MDPI AG, December 2020. [PUMA: RNA algorithm elements; hyper-stable prediction; scanning secondary structure]
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, June 2023. [PUMA: topic_lifescience (IMPs); (PCSs); (ncAAs); Click Integral Non-canonical Pseudocontact Rosetta; Structure acids amino chemistry; membrane prediction proteins shifts]