Author

K. Kappel

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Biophysics· 5 Biochemistry· 1

Signature Assays, Organisms & Methods

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Approach:deep learning· 5 Research Focus:protein structure prediction· 4 Approach:statistical model· 4 Assay:bulk RNA-seq· 2 Assay:cryo-EM· 2 Research Focus:protein design· 2 Assay:protein structure· 2 Research Focus:benchmarking· 1

Frequent Co-Authors

R. Das· 6 shared D. Herschlag· 2 shared I. Jarmoskaite· 2 shared P. P. Vaidyanathan· 2 shared S. K. Denny· 2 shared W. J. Greenleaf· 2 shared W. R. Becker· 2 shared A. Leaver-Fay· 1 shared

Activity by Year

2017-2019 · peak 3/yr

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10 top collaborators · 25 mutual co-author links

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6 shared papersBiophysics

R. Das

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6 papers

Recent·Most cited

Ribosolve: Rapid determination of three-dimensional RNA-only structures

K. Kappel, K. Zhang, Z. Su, W. Kladwang, S. Li, G. Pintilie, V. V. Topkar, R. Rangan, I. N. Zheludev, A. M. Watkins, J. D. Yesselman, W. Chiu, R. Das

Ribosolve rapidly determines 3D RNA-only structures using cryo-EM, chemical mapping, and Rosetta modeling, validated by multiple benchmarks and showing high accuracy.

bioRxiv · Jul 31, 2019Biophysics

Quantitative high-throughput tests of ubiquitous RNA secondary structure prediction algorithms via RNA/protein binding

W. R. Becker, I. Jarmoskaite, K. Kappel, P. P. Vaidyanathan, S. K. Denny, R. Das, W. J. Greenleaf, D. Herschlag

The paper quantitatively tests RNA secondary structure prediction algorithms using RNA-MaP, revealing significant deviations between predictions and experimental stabilities.

bioRxiv · Mar 8, 2019 · PreprintBiophysics

A quantitative and predictive model for RNA binding by human Pumilio proteins

I. Jarmoskaite, S. K. Denny, P. P. Vaidyanathan, W. R. Becker, J. O. L. Andreasson, C. J. Layton, K. Kappel, V. Shivashankar, R. Sreenivasan, R. Das, W. J. Greenleaf, D. Herschlag

The paper develops a predictive model for RNA binding by human PUM1 and PUM2 using RNA-MaP data, showing residue flipping and positional coupling, and validates it against in vivo crosslinking data.

bioRxiv · Aug 29, 2018Biochemistry

Sampling native-like structures of RNA-protein complexes through Rosetta folding and docking

K. Kappel, R. Das

The paper introduces RNP-denovo, a Rosetta method for folding and docking RNA to proteins, achieving native-like structures from low-resolution data.

bioRxiv · Jun 5, 2018Biophysics

De novo computational RNA modeling into cryoEM maps of large ribonucleoprotein complexes

K. Kappel, S. Liu, K. P. Larsen, G. Skiniotis, E. V. Puglisi, J. D. Puglisi, Z. H. Zhou, R. Zhao, R. Das

This paper introduces DRRAFTER, a method to model RNA-protein complexes from cryoEM maps, showing it can build accurate RNA coordinates in real-world scenarios.

bioRxiv · May 30, 2018Biophysics

The Rosetta all-atom energy function for macromolecular modeling and design

R. F. Alford, A. Leaver-Fay, J. R. Jeliazkov, M. J. O'Meara, F. P. DiMaio, H. Park, M. V. Shapovalov, P. D. Renfrew, V. K. Mulligan, K. Kappel, J. W. Labonte, M. S. Pacella, R. Bonneau, P. Bradley, R. L. Dunbrack, , J. J. Gray

The paper explains the Rosetta all-atom energy function, its mathematical models, and its application to biomolecular modeling and design, including new capabilities for membrane proteins and other macromolecules.

bioRxiv · Feb 7, 2017Biophysics