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» A graphical model for protein secondary structure prediction
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NAR
2007
90views more  NAR 2007»
13 years 8 months ago
The SUPERFAMILY database in 2007: families and functions
The SUPERFAMILY database provides protein domain assignments, at the SCOP ‘superfamily’ level, for the predicted protein sequences in over 400 completed genomes. A superfamily...
Derek Wilson, Martin Madera, Christine Vogel, Cyru...
CAGD
2006
120views more  CAGD 2006»
13 years 9 months ago
Quality meshing of implicit solvation models of biomolecular structures
This paper describes a comprehensive approach to construct quality meshes for implicit solvation models of biomolecular structures starting from atomic resolution data in the Prot...
Yongjie Zhang, Guoliang Xu, Chandrajit L. Bajaj
BMCBI
2007
142views more  BMCBI 2007»
13 years 9 months ago
Improving model construction of profile HMMs for remote homology detection through structural alignment
Background: Remote homology detection is a challenging problem in Bioinformatics. Arguably, profile Hidden Markov Models (pHMMs) are one of the most successful approaches in addre...
Juliana S. Bernardes, Alberto M. R. Dávila,...
BMCBI
2007
183views more  BMCBI 2007»
13 years 9 months ago
Considerations in the identification of functional RNA structural elements in genomic alignments
Background: Accurate identification of novel, functional noncoding (nc) RNA features in genome sequence has proven more difficult than for exons. Current algorithms identify and s...
Tomas Babak, Benjamin J. Blencowe, Timothy R. Hugh...
BMCBI
2008
123views more  BMCBI 2008»
13 years 9 months ago
Shape based indexing for faster search of RNA family databases
Background: Most non-coding RNA families exert their function by means of a conserved, common secondary structure. The Rfam data base contains more than five hundred structurally ...
Stefan Janssen, Jens Reeder, Robert Giegerich