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  1. No Access手机体育投注平台

    Protocol

    Inverse RNA Folding Workflow to Design and Test Ribozymes that Include Pseudoknots

    手机体育投注平台 Ribozymes are RNAs that catalyze reactions. They occur in nature, and can also be evolved in vitro to catalyze novel reactions. This chapter provides detailed protocols for using inverse folding software to de...

    Mohammad Kayedkhordeh, Ryota Yamagami, Philip C. Bevilacqua, David H. Mathews in Ribozymes (2021)

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    手机体育投注平台 Book

    RNA Structure Determination

    手机体育投注平台Methods and Protocols

    Douglas H. Turner, David H. Mathews in Methods in Molecular Biology (2016)

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    手机体育投注平台 Protocol

    Predicting RNA–RNA Interactions Using RNAstructure

    RNA–RNA binding is a required step for many regulatory and catalytic processes in the cell. Identifying RNA–RNA hybridization sites is challenging because of the competition between intramolecular and intermol...

    Laura DiChiacchio, David H. Mathews in RNA Structure Determination (2016)

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    手机体育投注平台 Protocol

    Prediction of Secondary Structures Conserved in Multiple RNA Sequences

    手机体育投注平台 RNA structure is conserved by evolution to a greater extent than sequence. Predicting the conserved structure for multiple homologous sequences can be much more accurate than predicting the structure for a sin...

    Zhenjiang Zech Xu, David H. Mathews in RNA Structure Determination (2016)

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    手机体育投注平台 Protocol

    Secondary Structure Prediction of Single Sequences Using RNAstructure

    手机体育投注平台 RNA secondary structure is often predicted using folding thermodynamics. RNAstructure is a software package that includes structure prediction by free energy minimization, prediction of base pairing probabilit...

    Zhenjiang Zech Xu, David H. Mathews in RNA Structure Determination (2016)

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    Protocol

    Experiment-Assisted Secondary Structure Prediction with RNAstructure

    手机体育投注平台 Experimental probing data can be used to improve the accuracy of RNA secondary structure prediction. The software package RNAstructure can take advantage of enzymatic cleavage data, FMN cleavage data, traditio...

    Zhenjiang Zech Xu, David H. Mathews in RNA Structure Determination (2016)

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    Protocol

    The Determination of RNA Folding Nearest Neighbor Parameters

    手机体育投注平台 The stability of RNA secondary structure can be predicted using a set of nearest neighbor parameters. These parameters are widely used by algorithms that predict secondary structure. This contribution introduc...

    Mirela Andronescu, Anne Condon in RNA Sequence, Structure, and Function: Com… (2014)

  8. Article

    Open Access

    Accelerating calculations of RNA secondary structure partition functions using GPUs

    RNA performs many diverse functions in the cell in addition to its role as a messenger of genetic information. These functions depend on its ability to fold to a unique three-dimensional structure determined b...

    Harry A Stern, David H Mathews in Algorithms for Molecular Biology (2013)

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    手机体育投注平台 Protocol

    RNA Structure Prediction: An Overview of Methods

    RNA is now appreciated to serve numerous cellular roles, and understanding RNA structure is important for understanding a mechanism of action. This contribution discusses the methods available for predicting R...

    Matthew G. Seetin, David H. Mathews in Bacterial Regulatory RNA (2012)

  10. 手机体育投注平台 Article

    Open Access

    TurboFold: Iterative probabilistic estimation of secondary structures for multiple RNA sequences

    The prediction of secondary structure, i.e. the set of canonical base pairs between nucleotides, is a first step in developing an understanding of the function of an RNA sequence. The most accurate computation...

    Arif O Harmanci, Gaurav Sharma, David H Mathews in BMC Bioinformatics (2011)

  11. 手机体育投注平台 Article

    Open Access

    RNAstructure: software for RNA secondary structure prediction and analysis

    To understand an RNA sequence's mechanism of action, the structure must be known. Furthermore, target RNA structure is an important consideration in the design of small interfering RNAs and antisense DNA oligo...

    Jessica S Reuter, David H Mathews in BMC Bioinformatics (2010)

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    Using OligoWalk to Identify Efficient siRNA Sequences

    手机体育投注平台 RNA interference (RNAi) has emerged as an important tool in science and in medicine. Small-interfering RNAs (siRNAs) can be used to knockdown gene expression of specific mRNAs. In practice, a number of factors...

    David H. Mathews in RNA Therapeutics (2010)

  13. 手机体育投注平台 Article

    Open Access

    Efficient pairwise RNA structure prediction using probabilistic alignment constraints in Dynalign

    手机体育投注平台 Joint alignment and secondary structure prediction of two RNA sequences can significantly improve the accuracy of the structural predictions. Methods addressing this problem, however, are forced to employ cons...

    Arif Ozgun Harmanci, Gaurav Sharma, David H Mathews in BMC Bioinformatics (2007)

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    手机体育投注平台 Article

    Predicting RNA secondary structure by free energy minimization

    RNA structure is hierarchical. Secondary structure contacts, i.e. the canonical base pair contacts, are generally stronger and form faster than the tertiary structure. Therefore, RNA secondary structures can b...

    David H. Mathews in Theoretical Chemistry Accounts (2006)

  15. Article

    Open Access

    Detection of non-coding RNAs on the basis of predicted secondary structure formation free energy change

    Non-coding RNAs (ncRNAs) have a multitude of roles in the cell, many of which remain to be discovered. However, it is difficult to detect novel ncRNAs in biochemical screens. To advance biological knowledge, c...

    Andrew V Uzilov, Joshua M Keegan, David H Mathews in BMC Bioinformatics (2006)