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BMCBI
2010
139views more  BMCBI 2010»
13 years 8 months ago
A global optimization algorithm for protein surface alignment
Background: A relevant problem in drug design is the comparison and recognition of protein binding sites. Binding sites recognition is generally based on geometry often combined w...
Paola Bertolazzi, Concettina Guerra, Giampaolo Liu...
GECCO
2010
Springer
189views Optimization» more  GECCO 2010»
13 years 5 months ago
Multiobjective evolutionary algorithm for software project portfolio optimization
Large software companies have to plan their project portfolio to maximize potential portfolio return and strategic alignment, while balancing various preferences, and considering ...
Thomas Kremmel, Jirí Kubalík, Stefan...
BMCBI
2006
120views more  BMCBI 2006»
13 years 8 months ago
Optimizing amino acid substitution matrices with a local alignment kernel
Background: Detecting remote homologies by direct comparison of protein sequences remains a challenging task. We had previously developed a similarity score between sequences, cal...
Hiroto Saigo, Jean-Philippe Vert, Tatsuya Akutsu
IJBRA
2006
111views more  IJBRA 2006»
13 years 8 months ago
Memory efficient alignment between RNA sequences and stochastic grammar models of pseudoknots
: Stochastic Context-Free Grammars (SCFG) has been shown to be effective in modelling RNA secondary structure for searches. Our previous work (Cai et al., 2003) in Stochastic Paral...
Yinglei Song, Chunmei Liu, Russell L. Malmberg, Co...
RECOMB
2004
Springer
14 years 8 months ago
Aligning alignments exactly
d abstract) John Kececioglu and Dean Starrett Department of Computer Science The University of Arizona Tucson AZ 85721, USA A basic computational problem that arises in both the...
John D. Kececioglu, Dean Starrett