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BMCBI
2006
120views more  BMCBI 2006»
13 years 8 months ago
Integrating protein structures and precomputed genealogies in the Magnum database: Examples with cellular retinoid binding prote
Background: When accurate models for the divergent evolution of protein sequences are integrated with complementary biological information, such as folded protein structures, anal...
Michael E. Bradley, Steven A. Benner
BMCBI
2006
141views more  BMCBI 2006»
13 years 8 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
2006
145views more  BMCBI 2006»
13 years 8 months ago
GEM System: automatic prototyping of cell-wide metabolic pathway models from genomes
Background: Successful realization of a "systems biology" approach to analyzing cells is a grand challenge for our understanding of life. However, current modeling appro...
Kazuharu Arakawa, Yohei Yamada, Kosaku Shinoda, Yo...
BMCBI
2006
102views more  BMCBI 2006»
13 years 8 months ago
UVPAR: fast detection of functional shifts in duplicate genes
Background: The imprint of natural selection on gene sequences is often difficult to detect. A plethora of methods have been devised to detect genetic changes due to selective pro...
Vicente Arnau, Miguel Gallach, J. Ignasi Lucas, Ig...
BMCBI
2006
94views more  BMCBI 2006»
13 years 8 months ago
Metabolite coupling in genome-scale metabolic networks
Background: Biochemically detailed stoichiometric matrices have now been reconstructed for various bacteria, yeast, and for the human cardiac mitochondrion based on genomic and pr...
Scott A. Becker, Nathan D. Price, Bernhard O. Pals...
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