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» On predicting secondary structure transition
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ISSPIT
2010
13 years 3 months 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
WABI
2010
Springer
128views Bioinformatics» more  WABI 2010»
13 years 7 months ago
Sparsification of RNA Structure Prediction Including Pseudoknots
Background: Although many RNA molecules contain pseudoknots, computational prediction of pseudoknotted RNA structure is still in its infancy due to high running time and space con...
Mathias Möhl, Raheleh Salari, Sebastian Will,...
BMCBI
2006
112views more  BMCBI 2006»
13 years 8 months ago
Distill: a suite of web servers for the prediction of one-, two- and three-dimensional structural features of proteins
Background: We describe Distill, a suite of servers for the prediction of protein structural features: secondary structure; relative solvent accessibility; contact density; backbo...
Davide Baù, Alberto J. M. Martin, Catherine...
BMCBI
2007
134views more  BMCBI 2007»
13 years 9 months ago
Efficient pairwise RNA structure prediction using probabilistic alignment constraints in Dynalign
Background: Joint alignment and secondary structure prediction of two RNA sequences can significantly improve the accuracy of the structural predictions. Methods addressing this p...
Arif Ozgun Harmanci, Gaurav Sharma, David H. Mathe...
DNA
2007
Springer
107views Bioinformatics» more  DNA 2007»
14 years 3 months ago
Autonomous Programmable Nanorobotic Devices Using DNAzymes
Abstract. A major challenge in nanoscience is the design of synthetic molecular devices that run autonomously and are programmable. DNA-based synthetic molecular devices have the a...
John H. Reif, Sudheer Sahu