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» Structured Sparsity in Structured Prediction
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BMCBI
2007
124views more  BMCBI 2007»
15 years 4 months ago
Protein structural similarity search by Ramachandran codes
Background: Protein structural data has increased exponentially, such that fast and accurate tools are necessary to access structure similarity search. To improve the search speed...
Wei-Cheng Lo, Po-Jung Huang, Chih-Hung Chang, Ping...
NAR
2010
129views more  NAR 2010»
14 years 11 months ago
PROSESS: a protein structure evaluation suite and server
PROSESS (PROtein Structure Evaluation Suite and Server) is a web server designed to evaluate and validate protein structures generated by X-ray crystallography, NMR spectroscopy o...
Mark V. Berjanskii, Yongjie Liang, Jianjun Zhou, P...
BMCBI
2006
141views more  BMCBI 2006»
15 years 4 months ago
Identification of consensus RNA secondary structures using suffix arrays
Background: The identification of a consensus RNA motif often consists in finding a conserved secondary structure with minimum free energy in an ensemble of aligned sequences. How...
Mohammad Anwar, Truong Nguyen, Marcel Turcotte
BMCBI
2004
208views more  BMCBI 2004»
15 years 4 months ago
Using 3D Hidden Markov Models that explicitly represent spatial coordinates to model and compare protein structures
Background: Hidden Markov Models (HMMs) have proven very useful in computational biology for such applications as sequence pattern matching, gene-finding, and structure prediction...
Vadim Alexandrov, Mark Gerstein
BMCBI
2008
140views more  BMCBI 2008»
15 years 4 months ago
Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework
Background: Structural alignment of RNAs is becoming important, since the discovery of functional non-coding RNAs (ncRNAs). Recent studies, mainly based on various approximations ...
Kazutaka Katoh, Hiroyuki Toh