A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2013; you can also visit the original URL.
The file type is application/pdf.
Filters
RNA Secondary Structure Prediction Via Energy Density Minimization
[chapter]
2006
Lecture Notes in Computer Science
Preserved Fulltext
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
2007
Nucleic Acids Research
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
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
2015
Bioinformatics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
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]
2006
Lecture Notes in Computer Science
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2007; you can also visit the original URL.
The file type is application/pdf.
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
2007
Journal of Computational Biology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2007; you can also visit the original URL.
The file type is application/pdf.
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
2009
Nucleic Acids Research
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2013; you can also visit the original URL.
The file type is application/pdf.
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
2008
Nucleic Acids Research
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2018; you can also visit the original URL.
The file type is application/pdf.
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]
2005
Lecture Notes in Computer Science
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2007; you can also visit the original URL.
The file type is application/pdf.
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]
2021
arXiv
pre-print
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
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
2009
Journal of Computer Science
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2011; you can also visit the original URL.
The file type is application/pdf.
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
2014
PLoS ONE
Preserved Fulltext
The Internet Archive has a preservation copy of this work in our general collections.
The file type is application/pdf.
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
2011
Journal of Molecular Biology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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
2018
Microbiology spectrum
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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]
2017
bioRxiv
pre-print
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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
2008
Bulletin of Mathematical Biology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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
« Previous
Showing results 1 — 15 out of 27,203 results