User profiles for Kalli Kappel

Kalli Kappel

HHMI Hanna Gray Fellow, Broad Institute of MIT and Harvard
Verified email at broadinstitute.org
Cited by 3032

Accelerated cryo-EM-guided determination of three-dimensional RNA-only structures

K Kappel, K Zhang, Z Su, AM Watkins, W Kladwang… - Nature …, 2020 - nature.com
The discovery and design of biologically important RNA molecules is outpacing three-dimensional
structural characterization. Here, we demonstrate that cryo-electron microscopy can …

Cryo-EM structures of full-length Tetrahymena ribozyme at 3.1 Å resolution

Z Su, K Zhang, K Kappel, S Li, MZ Palo, GD Pintilie… - Nature, 2021 - nature.com
Single-particle cryogenic electron microscopy (cryo-EM) has become a standard technique
for determining protein structures at atomic resolution 1 , 2 – 3 . However, cryo-EM studies of …

De novo computational RNA modeling into cryo-EM maps of large ribonucleoprotein complexes

K Kappel, S Liu, KP Larsen, G Skiniotis, EV Puglisi… - Nature …, 2018 - nature.com
Increasingly, cryo-electron microscopy (cryo-EM) is used to determine the structures of RNA–protein
assemblies, but nearly all maps determined with this method have biologically …

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

K Kappel, R Das - Structure, 2019 - cell.com
RNA-protein complexes underlie numerous cellular processes including translation, splicing,
and posttranscriptional regulation of gene expression. The structures of these complexes …

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

…, PD Renfrew, VK Mulligan, K Kappel… - Journal of chemical …, 2017 - ACS Publications
Over the past decade, the Rosetta biomolecular modeling suite has informed diverse
biological questions and engineering challenges ranging from interpretation of low-resolution …

Macromolecular modeling and design in Rosetta: recent methods and frameworks

…, TM Jacobs, JR Jeliazkov, DK Johnson, K Kappel… - Nature …, 2020 - nature.com
The Rosetta software for macromolecular modeling, docking and design is extensively used
in laboratories worldwide. During two decades of development by a community of …

RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme

…, S Dunin-Horkawicz, C Geniesse, K Kappel… - Rna, 2017 - rnajournal.cshlp.org
RNA-Puzzles is a collective experiment in blind 3D RNA structure prediction. We report
here a third round of RNA-Puzzles. Five puzzles, 4, 8, 12, 13, 14, all structures of riboswitch …

A unified mechanism for intron and exon definition and back-splicing

…, A Issaian, RC Hill, S Espinosa, S Shi, Y Cui, K Kappel… - Nature, 2019 - nature.com
The molecular mechanisms of exon definition and back-splicing are fundamental unanswered
questions in pre-mRNA splicing. Here we report cryo-electron microscopy structures of …

Accelerated molecular dynamics simulations of ligand binding to a muscarinic G-protein-coupled receptor

K Kappel, Y Miao, JA McCammon - Quarterly reviews of biophysics, 2015 - cambridge.org
Elucidating the detailed process of ligand binding to a receptor is pharmaceutically
important for identifying druggable binding sites. With the ability to provide atomistic detail, …

[HTML][HTML] Cryo-EM structure of a 40 kDa SAM-IV riboswitch RNA at 3.7 Å resolution

K Zhang, S Li, K Kappel, G Pintilie, Z Su… - Nature …, 2019 - nature.com
Specimens below 50 kDa have generally been considered too small to be analyzed by
single-particle cryo-electron microscopy (cryo-EM). The high flexibility of pure RNAs makes it …