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RNA Secondary Structure Prediction Via Energy Density Minimization [chapter]

Can Alkan, Emre Karakoc, S. Cenk Sahinalp, Peter Unrau, H. Alexander Ebhardt, Kaizhong Zhang, Jeremy Buhler
2006 Lecture Notes in Computer Science  
via free energy minimization.  ...  The vast majority of the computational tools for RNA secondary structure prediction are based on free energy minimization.  ...  Despite a 25 year long effort to perfect secondary structure prediction of a single RNA sequence via energy minimization, the end result is still far from perfect.  ... 
doi:10.1007/11732990_12 fatcat:fy3zwocdjze63kwio6dem7cm4m

taveRNA: a web suite for RNA algorithms and applications

C. Aksay, R. Salari, E. Karakoc, C. Alkan, S. C. Sahinalp
2007 Nucleic Acids Research  
It is based on a dynamic programming solution that minimizes the sum of energy density and free energy of an RNA structure. inteRNA is the first RNA-RNA interaction structure prediction web service.  ...  We present taveRNA, a web server package that hosts three RNA web services: alteRNA, inteRNA and pRuNA. alteRNA is a new alternative for RNA secondary structure prediction.  ...  thermodynamic approach to the RNA secondary structure prediction problem, which aims to minimize a linear combination of total free energy and total energy density using the dynamic programming formulation  ... 
doi:10.1093/nar/gkm303 pmid:17488837 pmcid:PMC1933159 fatcat:7kyaybqmjbexvmr5iyogury2hi

AccessFold: predicting RNA–RNA interactions with consideration for competing self-structure

Laura DiChiacchio, Michael F. Sloma, David H. Mathews
2015 Bioinformatics  
Free energy density minimization minimizes the folding free energy change per nucleotide involved in an intermolecular secondary structure.  ...  These algorithms utilize two novel approaches to evaluate accessibility: free energy density minimization and pseudo-energy minimization.  ...  Free energy density minimization In the free energy density minimization algorithm, DensityMin, the optimal structure is computed by finding the intermolecular structure with the lowest folding free energy  ... 
doi:10.1093/bioinformatics/btv682 pmid:26589271 pmcid:PMC4907385 fatcat:uf4br5liwzetpgkpii3mcwkdoe

A Study of Accessible Motifs and RNA Folding Complexity [chapter]

Ydo Wexler, Chaya Zilberstein, Michal Ziv-Ukelson
2006 Lecture Notes in Computer Science  
secondary structure prediction [24, 25, 43] .  ...  We speed up the dynamic programming algorithms that are standard for RNA folding prediction.  ...  This base-paired structure is called the secondary structure of the RNA. Base pairs almost always occur in a nested fashion in RNA secondary structure.  ... 
doi:10.1007/11732990_40 fatcat:j7urzyagn5c27bm4opo3p2nhm4

A Study of Accessible Motifs and RNA Folding Complexity

Ydo Wexler, Chaya Zilberstein, Michal Ziv-Ukelson
2007 Journal of Computational Biology  
secondary structure prediction [24, 25, 43] .  ...  We speed up the dynamic programming algorithms that are standard for RNA folding prediction.  ...  This base-paired structure is called the secondary structure of the RNA. Base pairs almost always occur in a nested fashion in RNA secondary structure.  ... 
doi:10.1089/cmb.2007.r020 pmid:17691898 fatcat:yzz5sna43vb35pan7k7qkcsmqy

In silico selection of RNA aptamers

Y. Chushak, M. O. Stone
2009 Nucleic Acids Research  
Our approach consists of three steps: (i) selection of RNA sequences based on their secondary structure, (ii) generating a library of three-dimensional (3D) structures of RNA molecules and (iii) high-throughput  ...  We developed a set of criteria that allows one to select a sequence with potential binding affinity from a pool of random sequences and developed a protocol for RNA 3D structure prediction.  ...  Jiang from the Biotechnology HPC Software Applications Institute for useful discussions about the 3D structure prediction and using DOVIS package for RNA-ligand docking.  ... 
doi:10.1093/nar/gkp408 pmid:19465396 pmcid:PMC2709588 fatcat:6cqnt73z2rfqbpynntdomwrreq

The Vienna RNA Websuite

A. R. Gruber, R. Lorenz, S. H. Bernhart, R. Neubock, I. L. Hofacker
2008 Nucleic Acids Research  
Among them, we find folding of single and aligned sequences, prediction of RNA-RNA interactions, and design of sequences with a given structure.  ...  Additionally, we provide analysis of folding landscapes using the barriers program and structural RNA alignments using LocARNA.  ...  This work was supported by the Austrian GEN-AU projects 'non coding RNA' and 'Bioinformatics Integration Network', as well as by the European Union as part of the FP-6 EMBIO project.  ... 
doi:10.1093/nar/gkn188 pmid:18424795 pmcid:PMC2447809 fatcat:64s4m2btk5d3xbsy7efa2r3bma

RNA-RNA Interaction Prediction and Antisense RNA Target Search [chapter]

Can Alkan, Emre Karakoç, Joseph H. Nadeau, S. Cenk Şahinalp, Kaizhong Zhang
2005 Lecture Notes in Computer Science  
Although there are a number of algorithms for predicting the secondary structure of a single RNA molecule, no such algorithm exists for reliably predicting the joint secondary structure of two interacting  ...  Our algorithms minimize the joint free-energy between the two RNA molecules under a number of energy models with growing complexity.  ...  The addition of four more parameters (and four new degrees of freedom) makes this approach more adjustable to specific properties of the input RNA strands.  ... 
doi:10.1007/11415770_12 fatcat:lmwv3k66erderdukgjcahu4rne

Predicting 3D RNA Folding Patterns via Quadratic Binary Optimization [article]

Mark W. Lewis, Amit Verma, Rick Hennig
2021 arXiv   pre-print
Many computer programs (known as in silico) are available for predicting 2-dimensional (secondary) structures however 3-dimensional (tertiary) structure prediction is much more difficult mainly due to  ...  Predicting structure given a one dimensional sequence of RNA nucleotide bases is a difficult and important problem.  ...  Secondly, inaccuracies in the energy function used by the RNA secondary structure prediction method may produce a false MFE.  ... 
arXiv:2106.07527v1 fatcat:xtjc6zvolzbddi6g3fne3upary

A Survey of Compute Intensive Algorithms for Ribo Nucleic Acids Structural Detection

Ra`ed M. Al-Khatib, Rosni Abdullah, Nur`Aini Abdul Rash
2009 Journal of Computer Science  
Results: Our findings of this survey confirmed that Dynamic Programming (DP) method via CMP algorithms can be used to predict the RNA secondary structure with simple PK and it gives good results.  ...  Approach: We computed various algorithms that predicted an RNA molecules secondary structure from primary sequence, without pseudoknots from one side and pseudoknotted RNA secondary structure in the other  ...  of structure internal loops by using RNA secondary structure prediction prediction from RNA by using energy rules.  ... 
doi:10.3844/jcssp.2009.680.689 fatcat:3nnefutdhvg5xmenpx6frv3zei

RNAthermsw: Direct Temperature Simulations for Predicting the Location of RNA Thermometers

Alexander Churkin, Assaf Avihoo, Michal Shapira, Danny Barash, Vladimir N. Uversky
2014 PLoS ONE  
It operates by analyzing dotted figures generated as a result of a moving window that performs successive energy minimization folding predictions.  ...  Also known as RNA thermosensors, these temperature-sensitive segments of the mRNA regulate gene expression by changing their secondary structure in response to temperature fluctuations.  ...  Storage of structures in RNA-SURIBA involved RNA secondary structure prediction by energy minimization using mfold [27] and dot bracket annotation together with relevant characteristics such as number  ... 
doi:10.1371/journal.pone.0094340 pmid:24718440 pmcid:PMC3981793 fatcat:d5piwlwgnfdxhpnjkctueslkjy

Thermodynamics and Kinetics of the Hairpin Ribozyme from Atomistic Folding/Unfolding Simulations

Lucas G. Nivón, Eugene I. Shakhnovich
2011 Journal of Molecular Biology  
This method should be useful in predicting folding transition states for many natural or man-made RNA tertiary structures.  ...  The hairpin ribozyme folds in solution and catalyzes self-cleavage or ligation via a specific two-domain structure.  ...  for both the minimal and full (four way junction, 4WJ) forms of the RNA.  ... 
doi:10.1016/j.jmb.2011.06.042 pmid:21740912 pmcid:PMC3508787 fatcat:dwomcg5up5ckxecpqf7nyhhd2u

Structure and Interaction Prediction in Prokaryotic RNA Biology

Patrick R. Wright*, Martin Mann*, Rolf Backofen*
2018 Microbiology spectrum  
In this review we technically outline thermodynamics-based standard RNA secondary structure and RNA-RNA interaction prediction approaches that have proven valuable to the RNA research community in the  ...  A structure P for a given RNA R can be encoded by its set of base pairs In the basic RNA secondary structure model, each base can form only a single base pairing within the molecule.  ...  Current RNA secondary structure prediction algorithms are usually energy minimization methods.  ... 
doi:10.1128/microbiolspec.rwr-0001-2017 pmid:29676245 fatcat:feq7paljxfejfglbd4fkows3we

Learning RNA secondary structure (only) from structure probing data [article]

Chuan-Sheng Foo, Cristina Pop
2017 bioRxiv   pre-print
We present CONTRAfold-SE, which extends CONTRAfold to model RNA structure-probing data as observations of possibly unknown secondary structures.  ...  We train CONTRAfold-SE on various combinations of structure probing data and complete structures and find that while genome-wide structure probing data provides modest improvement in prediction performance  ...  In general, statistical methods for RNA secondary structure prediction outperform energy-based methods [20, 18] .  ... 
doi:10.1101/152629 fatcat:uyjhurv6qrbpdomig74aobp46y

Large Deviations for Random Trees and the Branching of RNA Secondary Structures

Yuri Bakhtin, Christine E. Heitsch
2008 Bulletin of Mathematical Biology  
We calculate the typical degree distributions based on nearest neighbor free energies, and compare our results with the branching configurations found in two sets of large RNA secondary structures.  ...  We give a Large Deviation Principle (LDP) with explicit rate function for the distribution of vertex degrees in plane trees, a combinatorial model of RNA secondary structures.  ...  This is a challenging biological question since the accuracy of RNA secondary structure prediction methods by free energy minimization decreases with sequence length [6, 8, 13, 15, 26, 27] .  ... 
doi:10.1007/s11538-008-9353-y pmid:19083065 pmcid:PMC2834537 fatcat:5dignsfhdreglojw5ky5puiesy
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