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Kappel K, Strebinger D, Edmonds KHK, VO SCDT, Vockley CM, Biswas T, Farhi SL, Macrae R, Zhang F, Regev A. Characterizing protein sequence determinants of nuclear condensates by high-throughput pooled imaging with CondenSeq. Nature Methods. (2025). doi: https://doi.org/10.1038/s41592-025-02726-y PDF
Andress C, Kappel K, Villena ME, Cuperlovic-Culf M, Yan H, Li Y. DAPTEV: Deep aptamer evolutionary modelling for COVID-19 drug design. PLOS Computational Biology. (2023). doi: 10.1371/journal.pcbi.1010774 PDF
Hirano S*, Kappel K*, Altae-Tran H, Faure G, Wilkinson ME, Kannan S, Demircioglu FE, Yan R, Shiozaki M, Yu Z, Makarova KS, Koonin EV, Macrae RK, Zhang F. Structure of the OMEGA nickase IsrB in complex with ωRNA and target DNA. Nature. (2022). doi: 10.1038/s41586-022-05324-6 PDF
Ma H, Pham P, Luo B, Rangan R, Kappel K, Su Z, Das R. Auto-DRRAFTER: Automated RNA Modeling Based on Cryo-EM Density. Methods Mol Biol. (2022). doi: 10.1007/978-1-0716-2687-0_13 PDF
Li S, Palo MZ, Pintilie, G, Zhang X, Su Z, Kappel K, Chiu W, Zhang K, Das R. Topological crossing in the misfolded Tetrahymena ribozyme resolved by cryo-EM. PNAS. (2022). doi: 10.1073/pnas.2209146119 PDF
Su Z*, Zhang K*, Kappel K*, Li S, Palo MZ, Pintilie GD, Rangan R, Luo B, Wei Y, Das R, Chiu W. Cryo-EM structures of full-length Tetrahymena ribozyme at 3.1 Å resolution. Nature. (2021). doi: 10.1038/s41586-021-03803-w PDF
Liu X, Sun T, Shcherbina A, Li Q, Kappel K, Jarmoskaite I, Ramaswami G, Das R, Kundaje A, Li JB. Learning cis-regulatory principles of ADAR-based RNA editing from CRISPR-mediated mutagenesis. Nature Communications. (2021). doi: 10.1038/s41467-021-22489-2 PDF
Kappel K*, Zhang K*, Su Z*, Kladwang W, Li S, Pintilie G, Topkar VV, Rangan R, Zheludev IN, Yesselman JD, Chiu W, Das R. Accelerated cryo-EM-guided determination of three-dimensional RNA-only structures. Nature Methods. (2020). doi: 10.1038/s41592-020-0878-9 PDF
Larsen KP, Choi J, Jackson LN, Kappel K, Zhang J, Ha B, Chen DH, Puglisi EV. Distinct Conformational States Underlie Pausing during Initiation of HIV-1 Reverse Transcription. Journal of Molecular Biology. (2020). doi: 10.1016/j.jmb.2020.06.003 PDF
Leman JK, Weitzner BD, Lewis SM, et al., (Kappel K [42]). Macromolecular modeling and design in Rosetta: recent methods and frameworks. Nature Methods. (2020). doi: 10.1038/s41592-020-0848-2 PDF
Zhang K*, Li S*, Kappel K*, Pintilie G, Su Z, Mou TC, Schmid MF, Das R, Chiu W. Cryo-EM Structure of a 40-kDa SAM-IV Riboswitch RNA at 3.7 Å Resolution. Nature Communications. (2019). 10(1): 5511. doi: 10.1038/s41467-019-13494-7 PDF
Magnus M, Kappel K, Das R, Bujnicki J. RNA 3D structure prediction guided by independent folding of homologous sequences. BMC Bioinformatics. (2019). 20: 512; doi: 10.1186/s12859-019-3120-y PDF
Li X, Liu S, Zhang L, Issaian A, Hill RC, Espinosa S, Shi S, Cui Y, Kappel K, Das R, Hansen KC, Zhou ZH, Zhao R. A unified mechanism for intron and exon definition and back-splicing. Nature. (2019). 573: 375-380; doi: 10.1038/s41586-019-1523-6 PDF
Kappel K, Jarmoskaite I, Vaidyanathan PP, Greenleaf WJ, Herschlag D, Das R. Blind tests of RNA-protein binding affinity prediction. PNAS. (2019). 116: 8336-8341; doi: 10.1073/pnas.1819047116 PDF
Jarmoskaite I*, Denny SK*, Vaidyanathan PP*, Becker WR*, Andreasson JOL, Layton CJ, Kappel K, Shivashankar V, Sreenivasan R, Das R, Greenleaf WJ, Herschlag D. A quantitative and predictive model for RNA binding by human Pumilio proteins. Molecular Cell. (2019). 74: 966-981; doi: 10.1016/j.molcel.2019.04.012 PDF
Kappel K, Das R. Sampling native-like structures of RNA-protein complexes through Rosetta folding and docking. Structure. (2019). 27: 140-151; doi: 10.1016/j.str.2018.10.001 PDF
Kappel K, Liu S, Larsen KP, Skiniotis G, Puglisi EV, Puglisi JD, Zhou ZH, Zhao R, Das R. De novo computational RNA modeling into cryo-EM maps of large ribonucleoprotein complexes. Nature Methods. (2018). 15: 947–954; doi: 10.1038/s41592-018-0172-2 PDF
Larsen KP*, Mathiharan YK*, Kappel K, Coey AT, Chen DH, Barrero D, Madigan L, Puglisi JD, Skiniotis G, Puglisi EV. Architecture of an HIV-1 reverse transcriptase initiation complex. Nature. (2018). 557(7703): 118-122; doi: 10.1038/s41586-018-0055-9 PDF
Alford RF, Leaver-Fay A, Jeliazkov JR, O'Meara MJ, DiMaio FP, Park H, Shapovalov MV, Renfrew PD, Mulligan VK, Kappel K, Labonte JW, Pacella MS, Bonneau R, Bradley P, Dunbrack, Jr RL, Das R, Baker D, Kuhlman B, Kortemme T, Gray JJ. The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design. Journal of Chemical Theory and Computation. (2017). 13(6): 3031-3048; doi: 10.1021/acs.jctc.7b00125 PDF
Miao Z, Adamiak RW, Antczak M, et al. (Kappel K [19]). RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme. RNA. (2017). 23(5): 655-672; doi: 10.1261/rna.060368.116 PDF
Parks JW*, Kappel K*, Das R, Stone MD. Single molecule FRET-Rosetta reveals RNA structural rearrangements during human telomerase catalysis. RNA. (2017). 23(2): 175-188. doi: 10.1261/rna.058743.116 PDF
Chou FC, Kladwang W, Kappel K, Das R. Blind tests of RNA nearest-neighbor energy prediction. PNAS. (2016). 113(30): 8430-5; doi: 10.1073/pnas.1523335113 PDF
Kappel K, Miao Y, McCammon JA. Accelerated molecular dynamics simulations of ligand binding to a muscarinic G-protein coupled receptor. Quarterly Review of Biophysics. (2015). 48(4): 479-87; doi: 10.1017/S0033583515000153 PDF
Kappel K, Wereszczynski J, Clubb RT, McCammon JA. The binding mechanism, multiple binding modes, and allosteric regulation of Staphylococcus aureus Sortase A probed by molecular dynamics simulations. Protein Science. (2012). 21: 1858-1871; doi: 10.1002/pro.2168 PDF
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