Publications by authors named "R Kretsch"
Article Synopsis
- - RNA-Puzzles is a collaborative project focused on improving the prediction of RNA three-dimensional structures, with predictions made by modeling groups before experimental structures are published.
- - A significant set of predictions was made by 18 groups for 23 different RNA structures, including various elements like ribozymes and aptamers.
- - The study highlights key challenges in RNA modeling, such as identifying helix pairs and ensuring proper stacking, and notes that some top-performing groups also excelled in a separate competition (CASP15).
Article Synopsis
- The prediction of RNA structure from its sequence is challenging due to a lack of experimental data, which has slowed advancement in the field.
- Researchers have developed a dataset called Ribonanza, consisting of chemical mapping data from two million RNA sequences, collected through crowdsourcing platforms like Eterna.
- Utilizing this dataset, they created a deep learning model named RibonanzaNet, which, when fine-tuned, demonstrates superior performance in predicting various RNA behaviors, potentially improving understanding of RNA structures.
Tertiary folds of the SL5 RNA from the 5' proximal region of SARS-CoV-2 and related coronaviruses.
Proc Natl Acad Sci U S A
March 2024
Coronavirus genomes sequester their start codons within stem-loop 5 (SL5), a structured, 5' genomic RNA element. In most alpha- and betacoronaviruses, the secondary structure of SL5 is predicted to contain a four-way junction of helical stems, some of which are capped with UUYYGU hexaloops. Here, using cryogenic electron microscopy (cryo-EM) and computational modeling with biochemically determined secondary structures, we present three-dimensional structures of SL5 from six coronaviruses.
View Article and Find Full Text PDFCoronavirus genomes sequester their start codons within stem-loop 5 (SL5), a structured, 5' genomic RNA element. In most alpha- and betacoronaviruses, the secondary structure of SL5 is predicted to contain a four-way junction of helical stems, some of which are capped with UUYYGU hexaloops. Here, using cryogenic electron microscopy (cryo-EM) and computational modeling with biochemically-determined secondary structures, we present three-dimensional structures of SL5 from six coronaviruses.
View Article and Find Full Text PDFCASP assessments primarily rely on comparing predicted coordinates with experimental reference structures. However, experimental structures by their nature are only models themselves-their construction involves a certain degree of subjectivity in interpreting density maps and translating them to atomic coordinates. Here, we directly utilized density maps to evaluate the predictions by employing a method for ranking the quality of protein chain predictions based on their fit into the experimental density.
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