RNA-Puzzles: a CASP-like evaluation of RNA three-dimensional structure prediction.

By José Almeida Cruz, Marc-Frédérick Blanchet, Michal J. Boniecki, J. M. Bujnicki, Shi-Jie Chen, Song Cao, Rhiju Das, Feng Ding, N. V. Dokholyan, Samuel Flores and 23 more. 2012

150 citations recorded by the source corpus.

Subfields: Molecular Biology

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Citations in the corpus

Assessment of three-dimensional RNA structure prediction in CASP15 (2023, neutral): “However, it was not until 2011 that a regular assessment of models, called RNA-Puzzles, was set up.(7,8) The models for the RNA sequence of each RNA-Puzzle were collected prior to publications of the X-ray structures Since not enough targets were available for a short CASPlike season, the Puzzles we”
Accurate RNA 3D structure prediction using a language model-based deep learning approach (2022, positive): “To show that the promising results on RNA-Puzzles did not arise from overfitting, we studied whether the sequence similarity between the test set and our training data was substantially positively correlated with the performance of RhoFold+, as measured by the TM score and the local distance differe”
FARFAR2: Improved de novo Rosetta prediction of complex global RNA folds (2020, unknown): “Through our participation in the RNA-Puzzles trials (Cruz et al., 2012; Miao et al., 2015, 2017), we have kept records of our strategies for each prediction challenge, including secondary structure predictions, inferences based on homology to prior deposited structures, and functional constraints, s”
Protein Modelling: What Happened to the “Protein Structure Gap”? (2013, unknown): “…for protein modeling such as homology modeling, de novo prediction, quality estimation, or blind assessment of prediction methods, appear to be applicable with small adaptations to RNA structure modeling (Cruz et al., 2012; Rother et al., 2011; Seetin and Mathews, 2012; Sim et al., 2012).”
MCQ4Structures to compute similarity of molecule structures (2013, methodology): “4 we describe the results of MCQ4Structures experimental runs over a set of structures, including models submitted to RNA-Puzzles contest.”
Modeling complex RNA tertiary folds with Rosetta. (2015, methodology): “A homolog of this domain was posed as an RNA-Puzzles challenge (Cruz et al., 2012), and crystallographic and biochemical work on this system by several RNA laboratories (Butler, Xiong, Wang, & Strobel, 2011; Cordero, Kladwang, VanLang, & Das, 2012; Erion & Strobel, 2011; Kladwang, VanLang, Cordero,…”
RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures (2015, methodology): “This stage was very similar to that which they used previously in RNA-Puzzles (Cruz et al. 2012).”
ATOM3D: Tasks On Molecules in Three Dimensions (2020, methodology): “The RNA Puzzles competition [Cruz et al., 2012] is a rolling international competition dealing with the RNA structure prediction problem.”
De Novo RNA Tertiary Structure Prediction at Atomic Resolution Using Geometric Potentials from Deep Learning (2022, methodology): “To further examine DeepFoldRNA with the state of the art, we tested it on 17 challenging RNA targets from the community-wide RNA-Puzzles experiment, where many of the targets lacked structural and sequence homologs 6,7,13,19 .”
RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme (2017, methodology): “Data were distributed via the private RNA-Puzzles website or via entries with anonymized sequences in the RNA Mapping Database (Cordero et al. 2012); deposition IDs are summarized in Supplemental Table S8.”
SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction (2015, methodology): “These structures are generally very difficult to model, which is why the RNA Puzzles challenge is so important for the community of researchers working on RNA 3D structure prediction (13,40).”