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» iFoldRNA: three-dimensional RNA structure prediction and fol...
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RECOMB
2011
Springer
12 years 8 months ago
Rich Parameterization Improves RNA Structure Prediction
Motivation. Current approaches to RNA structure prediction range from physics-based methods, which rely on thousands of experimentally-measured thermodynamic parameters, to machin...
Shay Zakov, Yoav Goldberg, Michael Elhadad, Michal...
BIOINFORMATICS
2006
130views more  BIOINFORMATICS 2006»
13 years 5 months ago
Memory efficient folding algorithms for circular RNA secondary structures
A small class of RNA molecules, in particular the tiny genomes of viroids, are circular. Yet most structure prediction algorithms handle only linear RNAs. The most straightforward ...
Ivo L. Hofacker, Peter F. Stadler
ISSPIT
2010
13 years 17 days ago
Accelerating the Nussinov RNA folding algorithm with CUDA/GPU
Graphics processing units (GPU) on commodity video cards have evolved into powerful computational devices. The RNA secondary structure arises from the primary structure and a backb...
Dar-Jen Chang, Christopher Kimmer, Ming Ouyang
CANDC
2006
ACM
13 years 5 months ago
An RNA folding algorithm including pseudoknots based on dynamic weighted matching
On the basis of maximum weighted matching (MWM) algorithm, we introduced a dynamic weight related with stem length and used a recursive algorithm to predict RNA secondary structur...
Haijun Liu, Dong Xu, Jianlin Shao, Yifei Wang
HPDC
2010
IEEE
13 years 6 months ago
Exploring the RNA folding energy landscape using scalable distributed cyberinfrastructure
The increasing significance of RNAs in transcriptional or post-transcriptional gene regulation processes has generated considerable interest towards the prediction of RNA folding ...
Joohyun Kim, Wei Huang, Sharath Maddineni, Fareed ...