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WABI
2005
Springer
14 years 4 months ago
Rotamer-Pair Energy Calculations Using a Trie Data Structure
Abstract. Protein design software places amino acid side chains by precomputing rotamer-pair energies and optimizing rotamer placement. If the software optimizes by rapid stochasti...
Andrew Leaver-Fay, Brian Kuhlman, Jack Snoeyink
WABI
2005
Springer
14 years 4 months ago
Reaction Motifs in Metabolic Networks
Vincent Lacroix, Cristina G. Fernandes, Marie-Fran...
WABI
2005
Springer
14 years 4 months ago
A Unifying Framework for Seed Sensitivity and Its Application to Subset Seeds
Gregory Kucherov, Laurent Noé, Mikhail A. R...
WABI
2005
Springer
120views Bioinformatics» more  WABI 2005»
14 years 4 months ago
A Compressed Format for Collections of Phylogenetic Trees and Improved Consensus Performance
Phylogenetic tree searching algorithms often produce thousands of trees which biologists save in Newick format in order to perform further analysis. Unfortunately, Newick is neithe...
Robert S. Boyer, Warren A. Hunt Jr., Serita M. Nel...
WABI
2005
Springer
132views Bioinformatics» more  WABI 2005»
14 years 4 months ago
Perfect Sorting by Reversals Is Not Always Difficult
—We propose new algorithms for computing pairwise rearrangement scenarios that conserve the combinatorial structure of genomes. More precisely, we investigate the problem of sort...
Sèverine Bérard, Anne Bergeron, Cedr...
WABI
2005
Springer
120views Bioinformatics» more  WABI 2005»
14 years 4 months ago
Multiple Structural RNA Alignment with Lagrangian Relaxation
In contrast to proteins, many classes of functionally related RNA molecules show a rather weak sequence conservation but instead a fairly well conserved secondary structure. Hence ...
Markus Bauer, Gunnar W. Klau, Knut Reinert
WABI
2005
Springer
117views Bioinformatics» more  WABI 2005»
14 years 4 months ago
Pattern Identification in Biogeography
—Identifying common patterns among area cladograms that arise in historical biogeography is an important tool for biogeographical inference. We develop the first rigorous formali...
Ganeshkumar Ganapathy, Barbara Goodson, Robert K. ...