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: membrane Click proteins (IMPs); acids Non-canonical amino (ncAAs); topic_lifescience (PCSs); shifts prediction Structure Integral Pseudocontact Rosetta; chemistry;]
Biasing AlphaFold2 to predict GPCRs and kinases with user-defined functional or structural properties. Front. Mol. Biosci., (10):1121962, February 2023. [PUMA: (G-protein-coupled receptors); protein GPCRs kinases; topic_lifescience prediction function; AlphaFold; structure]
Benchmarking AlphaFold2 on peptide structure prediction. Structure, (31)1:111--119.e2, Elsevier BV, January 2023. [PUMA: bonds; benchmark; folding; peptides; AlphaFold2; disulfide protein topic_lifescience prediction pLDDT; structure]
Modeling of protein conformational changes with Rosetta guided by limited experimental data. Structure, (30)8:1157--1168.e3, Elsevier BV, August 2022. [PUMA: molecular EPR dynamics; biology; integrative structure modeling; structural protein changes; topic_lifescience refinement conformational spectroscopy; Rosetta;]
RosettaCM for antibodies with very long HCDR3s and low template availability. Proteins, (89)11:1458--1472, Wiley, November 2021. [PUMA: benchmark; homology modeling; loop prediction; topic_lifescience antibody; Rosetta; structure]
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: multitask convolutional prediction; memory transmembrane deep learning; neural networks; topology long short-term structure secondary topic_lifescience prediction]