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JCB
2000
146views more  JCB 2000»
9 years 1 months ago
Bayesian Segmentation of Protein Secondary Structure
We present a novel method for predicting the secondary structure of a protein from its amino acid sequence. Most existing methods predict each position in turn based on a local wi...
Scott C. Schmidler, Jun S. Liu, Douglas L. Brutlag
BMCBI
2004
133views more  BMCBI 2004»
9 years 1 months ago
Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure prediction
Background: RNA secondary structure prediction methods based on probabilistic modeling can be developed using stochastic context-free grammars (SCFGs). Such methods can readily co...
Robin D. Dowell, Sean R. Eddy
JCO
2007
149views more  JCO 2007»
9 years 1 months ago
A 2-approximation for the preceding-and-crossing structured 2-interval pattern problem
The 2-interval pattern problem over its various models and restrictions was proposed by Vialette (2004) for the application of RNA secondary structure prediction. We present an O(n...
Minghui Jiang
BMCBI
2006
137views more  BMCBI 2006»
9 years 1 months ago
Improving the accuracy of protein secondary structure prediction using structural alignment
Background: The accuracy of protein secondary structure prediction has steadily improved over the past 30 years. Now many secondary structure prediction methods routinely achieve ...
Scott Montgomerie, Shan Sundararaj, Warren J. Gall...
BMCBI
2006
102views more  BMCBI 2006»
9 years 1 months ago
Protein secondary structure prediction for a single-sequence using hidden semi-Markov models
Background: The accuracy of protein secondary structure prediction has been improving steadily towards the 88% estimated theoretical limit. There are two types of prediction algor...
Zafer Aydin, Yucel Altunbasak, Mark Borodovsky
BMCBI
2008
116views more  BMCBI 2008»
9 years 1 months ago
Impact of residue accessible surface area on the prediction of protein secondary structures
Background: The problem of accurate prediction of protein secondary structure continues to be one of the challenging problems in Bioinformatics. It has been previously suggested t...
Amir Momen-Roknabadi, Mehdi Sadeghi, Hamid Pezeshk...
BMCBI
2010
139views more  BMCBI 2010»
9 years 1 months ago
RNAstructure: software for RNA secondary structure prediction and analysis
Background: 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...
Jessica S. Reuter, David H. Mathews
BIOINFORMATICS
2010
87views more  BIOINFORMATICS 2010»
9 years 1 months ago
Improving protein secondary structure prediction using a simple k-mer model
Motivation: Existing methods for protein sequence analysis are generally firstorder and inherently assume that each position is independent. We develop a general framework for int...
Martin Madera, Ryan Calmus, Grant Thiltgen, Kevin ...
SIGIR
2004
ACM
9 years 6 months ago
Context sensitive vocabulary and its application in protein secondary structure prediction
Protein secondary structure prediction is an important step towards understanding the relation between protein sequence and structure. However, most current prediction methods use...
Yan Liu, Jaime G. Carbonell, Judith Klein-Seethara...
CEC
2005
IEEE
9 years 7 months ago
Evolving hidden Markov models for protein secondary structure prediction
New results are presented for the prediction of secondary structure information for protein sequences using Hidden Markov Models (HMMs) evolved using a Genetic Algorithm (GA). We a...
Kyoung-Jae Won, Thomas Hamelryck, Adam Prügel...
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