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Inverse Folding of RNA Pseudoknot Structures [article]

James Z.M. Gao and Linda Y.M. Li and Christian M. Reidys
2010 arXiv   pre-print
Conclusions: The algorithm Inv extends inverse folding capabilities to RNA pseudoknot structures.  ...  Since the established inverse folding algorithms, RNAinverse, RNA-SSD as well as INFO-RNA are limited to RNA secondary structures, we present in this paper the inverse folding algorithm Inv which can deal  ...  As discussed in the introduction it has to be given an argument as to why the inverse folding of pseudoknot RNA structures works.  ... 
arXiv:1003.2015v1 fatcat:7gznzumu5fhuroahy6yelmu7oa

Inverse folding of RNA pseudoknot structures [article]

James Z. M. Gao, Linda Y. M. Li, Christian M. Reidys
2010 arXiv   pre-print
Conclusions: The algorithm Inv extends inverse folding capabilities to RNA pseudoknot structures.  ...  Since the established inverse folding algorithms, RNAinverse, RNA-SSD as well as INFO-RNA are limited to RNA secondary structures, we present in this paper the inverse folding algorithm Inv which can deal  ...  As discussed in the introduction it has to be given an argument as to why the inverse folding of pseudoknot RNA structures works.  ... 
arXiv:0905.0733v2 fatcat:hxc7depmgvdufp62f3j2j2v3ce

Inverse folding of RNA pseudoknot structures

James ZM Gao, Linda YM Li, Christian M Reidys
2010 Algorithms for Molecular Biology  
Conclusions: The algorithm Inv extends inverse folding capabilities to RNA pseudoknot structures.  ...  Since the established inverse folding algorithms, RNAinverse, RNA-SSD as well as INFO-RNA are limited to RNA secondary structures, we present in this paper the inverse folding algorithm Inv which can deal  ...  This work was supported by the 973 Project, the PCSIRT of the Ministry of Education, the Ministry of Science and Technology, and the National Science Foundation of China.  ... 
doi:10.1186/1748-7188-5-27 pmid:20573197 pmcid:PMC2909241 fatcat:birgl2ay7rfnbpcvbbpr6g43um

Multi-Objective Genetic Algorithm for Pseudoknotted RNA Sequence Design

Akito Taneda
2012 Frontiers in Genetics  
the inverse folding of pseudoknotted RNAs.  ...  Although pseudoknots are functionally important motifs in RNA structures, less reports concerning the inverse folding of pseudoknotted RNAs have been done compared to those for pseudoknot-free RNA design  ...  Inv is an RNA inverse folding algorithm designed for a restricted pseudoknot class and can perform the inverse folding of pseudoknotted RNAs.  ... 
doi:10.3389/fgene.2012.00036 pmid:22558001 pmcid:PMC3337422 fatcat:x62whpbm2bhqrgoea6ycheysau

antaRNA – Multi-objective inverse folding of pseudoknot RNA using ant-colony optimization

Robert Kleinkauf, Torsten Houwaart, Rolf Backofen, Martin Mann
2015 BMC Bioinformatics  
Currently the design of RNA molecules, which fold into a specific structure (known as RNA inverse folding) within biotechnological applications, is lacking the feature of incorporating pseudoknot structures  ...  Many functional RNA molecules fold into pseudoknot structures, which are often essential for the formation of an RNA's 3D structure.  ...  Funding: This work was supportively funded by the Baden-Württemberg Ministry of Scielnce, Research and Arts (MWK grant 7533-7-11.6.1 Ideenwettbewerb Biotechnologie und Medizintechnik Baden-Württemberg  ... 
doi:10.1186/s12859-015-0815-6 pmid:26581440 pmcid:PMC4652366 fatcat:lixtj6kayrfpzplfs4bzcknk2e

ENTRNA: a framework to predict RNA foldability

Congzhe Su, Jeffery D. Weir, Fei Zhang, Hao Yan, Teresa Wu
2019 BMC Bioinformatics  
Existing literature has focused on RNA design as either an RNA structure prediction problem or an RNA inverse folding problem where free energy has played a key role.  ...  This new construct has the potential for both RNA structure prediction and the inverse folding problem. In addition, this new construct enables us to explore data-driven approaches in RNA research.  ...  In general, RNA secondary structure research falls into two categories: The RNA structure prediction problem, which is to predict the folding result of base pairs given the RNA sequence; and the RNA inverse  ... 
doi:10.1186/s12859-019-2948-5 fatcat:c2eetulg4ng4herhhm5lwvufdm

Design of highly active double-pseudoknotted ribozymes: a combined computational and experimental study

Ryota Yamagami, Mohammad Kayedkhordeh, David H Mathews, Philip C Bevilacqua
2018 Nucleic Acids Research  
Inverse folding for RNAs, which allows computational design of sequences that adopt specific structures, can be utilized for unveiling RNA functions and developing genetic tools in synthetic biology.  ...  Although many algorithms for inverse RNA folding have been developed, the pseudoknot, which plays a key role in folding of ribozymes and riboswitches, is not addressed in most algorithms.  ...  ACKNOWLEDGEMENTS We thank Kyle Messina for kind gifts of pH buffer for the rate-pH experiments, and the members of the Bevilacqua laboratory for valuable discussion.  ... 
doi:10.1093/nar/gky1118 pmid:30462314 pmcid:PMC6326823 fatcat:tfdemjxmmbdgnjdp5pofkw7ffi

Resected RNA pseudoknots and their recognition by histidyl-tRNA synthetase

B. Felden, R. Giege
1998 Proceedings of the National Academy of Sciences of the United States of America  
Design of this RNA fold is linked to the mimicry of the pseudoknotted amino acid accepting branch of the tRNA-like domain from brome mosaic virus, known to be charged by tyrosyl-tRNA synthetases, with  ...  Prediction of the histidylation function of the new family of minimalist tRNA-like structures relates to the geometry of resected pseudoknots that allows proper presentation to histidyl-tRNA synthetase  ...  FIG. 1 . 1 Design of a resected RNA pseudoknot by analogy with the tRNA-like structure of BMV RNA.  ... 
doi:10.1073/pnas.95.18.10431 pmid:9724720 pmcid:PMC27911 fatcat:r3p7p54wgnbydl7uf4slzq2xwq

RNA inverse folding using Monte Carlo tree search

Xiufeng Yang, Kazuki Yoshizoe, Akito Taneda, Koji Tsuda
2017 BMC Bioinformatics  
State-of-the-art RNA inverse folding algorithms can design simple and short RNA sequences of specific GC content, that fold into the target RNA structure.  ...  Using common benchmark datasets for evaluation, MCTS-RNA showed a lot of promise as a standard method of RNA inverse folding. Conclusion: MCTS-RNA is available at https://github.com/tsudalab/MCTS-RNA.  ...  The source code of MCTS-RNA is available at https://github.com/ tsudalab/MCTS-RNA. 1  ... 
doi:10.1186/s12859-017-1882-7 pmid:29110632 pmcid:PMC5674771 fatcat:wrrlzlob7vbz3aui7cd3rognxm

Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots

C. E. Hajdin, S. Bellaousov, W. Huggins, C. W. Leonard, D. H. Mathews, K. M. Weeks
2013 Proceedings of the National Academy of Sciences of the United States of America  
Nearly all RNAs can fold to form some secondary structure and, in many RNAs, highly structured regions encode important regulatory motifs.  ...  Among the best characterized of these specialized structures are RNA pseudoknots. Pseudoknots are relatively rare but occur overwhelmingly in functionally important regions of RNA (2-4).  ...  This work was supported by Grants AI068462 (to K.M.W.) and GM076485 (to D.H.M.) from the National Institutes of Health.  ... 
doi:10.1073/pnas.1219988110 pmid:23503844 pmcid:PMC3619282 fatcat:dfjsolygy5hirjun2b6miytwua

Mutational study reveals that tertiary interactions are conserved in ribosomal frameshifting pseudoknots of two luteoviruses

YANG-GYUN KIM, STEFAN MAAS, STEPHANIE C. WANG, ALEXANDER RICH
2000 RNA: A publication of the RNA Society  
argues for the pseudoknot to be the structural motif necessary for the frameshifting function in PLRV transcripts.  ...  It has been shown to harbor two signals, one active on the level of the primary structure, termed the slippery sequence, and one component that forms a secondary or tertiary level structure, described  ...  ACKNOWLEDGMENTS We have profited from discussions with B+ Brown, M+ Egli, K+ Lowenhaupt, and L+ Su+ This research was supported by grants from the National Institutes of Health, the National Science Foundation  ... 
doi:10.1017/s1355838200000510 pmid:10943894 pmcid:PMC1369989 fatcat:3xgnov6yw5hcxfr5gdhm7hhjo4

Multi-objective optimization for RNA design with multiple target secondary structures

Akito Taneda
2015 BMC Bioinformatics  
Results: We developed a novel computational tool for automatically designing RNA sequences which fold into multiple target secondary structures.  ...  We benchmarked our multi-target RNA design algorithm with the datasets of two, three, and four target structures and found that our algorithm shows better or comparable design performances compared with  ...  cannot perform the RNA inverse folding with multiple target structures.  ... 
doi:10.1186/s12859-015-0706-x pmid:26335276 pmcid:PMC4559319 fatcat:onlwien6grfjtgvvvww7nkxeve

Sequence-structure relations of biopolymers [article]

Christopher Barrett, Fenix W. Huang, Christian M. Reidys
2016 arXiv   pre-print
Motivation: DNA data is transcribed into single-stranded RNA, which folds into specific molecular structures.  ...  Results: We compute the partition function of sequences with respect to a fixed structure and connect this computation to the mutual information of a sequence-structure pair for RNA secondary structures  ...  Many thanks for the constructive feedback of the anonymous reviewers and their suggestions.  ... 
arXiv:1511.03141v2 fatcat:oh4onyucs5b4xl45ysmoyj2hve

Mechanical unfolding kinetics of the SRV-1 gag-pro mRNA pseudoknot: possible implications for −1 ribosomal frameshifting stimulation

Zhensheng Zhong, Lixia Yang, Haiping Zhang, Jiahao Shi, J. Jeya Vandana, Do Thuy Uyen Ha Lam, René C. L. Olsthoorn, Lanyuan Lu, Gang Chen
2016 Scientific Reports  
An RNA pseudoknot structure located in the overlapping region of the gag and pro genes of Simian Retrovirus type 1 (SRV-1) stimulates frameshifting.  ...  However, the experimental characterization of SRV-1 pseudoknot (un)folding dynamics and the effect of the base triple formation is lacking.  ...  Acknowledgements This work was supported by Singapore Ministry of Education (MOE) Tier 1 (RGT3/13 to G.C.) and MOE Tier  ... 
doi:10.1038/srep39549 pmid:28000744 pmcid:PMC5175198 fatcat:coyu5zkdevbwhmktaccmy3nawa

Structure-Altering Mutations of the SARS-CoV-2 Frame Shifting RNA Element [article]

Tamar Schlick, Qiyao Zhu, Swati Jain, Shuting Yan
2020 biorxiv/medrxiv  
Specifically, using RAG machinery of genetic algorithms for inverse folding adapted for RNA structures with pseudoknots, we computationally predict minimal mutations that destroy a structurally-important  ...  In this work, we apply our graph-theory-based framework for representing RNA secondary structures, "RAG" (RNA-As Graphs), to alter key structural features of the FSE of the SARS-CoV-2 virus.  ...  ACKNOWLEDGMENTS We gratefully acknowledge funding from the National Science Foundation RAPID Award 2030377 from the Division of Mathematical Science and the Division of Chemistry; National Institutes of  ... 
doi:10.1101/2020.08.28.271965 pmid:32869017 pmcid:PMC7457599 fatcat:crf2f4liy5febadblrorhrqfeq
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