Results 1 to 10 of about 9,541,112 (326)
RNA tertiary structure modeling with BRiQ potential in CASP15
bioRxiv, 2023 We describe the modeling method for RNA tertiary structures employed by team AIchemy_RNA2 in the 15th Critical Assessment of Protein Structure Prediction (CASP15). The method consists of the following steps.
Ke Chen +3 more
semanticscholar +2 more sources
Salt contribution to RNA tertiary structure folding stability. [PDF]
Biophys J, 2011 Accurate quantification of the ionic contribution to RNA folding stability could greatly enhance our ability to understand and predict RNA functions. Recently, motivated by the potential importance of ion correlation and fluctuation in RNA folding, we developed the tightly bound ion (TBI) model.
Zhi-Jie Tan, Shi-Jie Chen
semanticscholar +5 more sources
Automated RNA Tertiary Structure Prediction from Secondary Structure and Low-Resolution Restraints
Journal of Computational Chemistry, 2011 A novel protocol for all‐atom RNA tertiary structure prediction is presented that uses restrained molecular mechanics and simulated annealing. The restraints are from secondary structure, covariation analysis, coaxial stacking predictions for helices in ...
Matthew G. Seetin, D. Mathews
semanticscholar +3 more sources
Manipulating Zika virus RNA tertiary structure for developing tissue-specific attenuated vaccines [PDF]
EMBO Molecular MedicineTraditional live attenuated vaccines (LAVs) are typically developed through serial passaging or genetic engineering to introduce specific mutations or deletions.
Xiang Chen +10 more
doaj +2 more sources
Structural 3D Domain Reconstruction of the RNA Genome from Viruses with Secondary Structure Models
Viruses, 2021 Three-dimensional RNA domain reconstruction is important for the assembly, disassembly and delivery functionalities of a packed proteinaceus capsid. However, to date, the self-association of RNA molecules is still an open problem. Recent chemical probing
Simón Poblete, Horacio V. Guzman
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bioRxiv, 2022 Experimental characterization of RNA structure remains difficult, especially for non-coding RNAs that are critical to many cellular activities. We developed DeepFoldRNA to predict RNA structures from sequence alone by coupling deep self-attention neural ...
Robin Pearce, G. Omenn, Yang Zhang
semanticscholar +1 more source
RNA tertiary structure prediction using RNAComposer in CASP15
Proteins: Structure, Function, and Bioinformatics, 2023 As CASP15 participants, in the new category of 3D RNA structure prediction, we applied expert modeling with the support of our proprietary system RNAComposer. Although RNAComposer is primarily known as an automated web server, its features allow it to be
J. Sarzynska +3 more
semanticscholar +1 more source
RNAGCN: RNA tertiary structure assessment with a graph convolutional network
Chinese Physics B, 2022 RNAs play crucial and versatile roles in cellular biochemical reactions. Since experimental approaches of determining their three-dimensional (3D) structures are costly and less efficient, it is greatly advantageous to develop computational methods to ...
Cheng-Wei Deng +5 more
semanticscholar +1 more source
Deep Learning in RNA Structure Studies
Frontiers in Molecular Biosciences, 2022 Deep learning, or artificial neural networks, is a type of machine learning algorithm that can decipher underlying relationships from large volumes of data and has been successfully applied to solve structural biology questions, such as RNA structure ...
Haopeng Yu, Yiman Qi, Yiliang Ding
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Viruses, 2023 Enterovirus-D68 (EV-D68) is a positive-sense single-stranded RNA virus within the family Picornaviridae. EV-D68 was initially considered a respiratory virus that primarily affected children.
Connor Eastman, William E. Tapprich
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