Alain Deschênes

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This work presents a coarse-grained distributed genetic algorithm (GA) for RNA secondary structure prediction. This research builds on previous work and contains two new thermodynamic models, INN and INN-HB, which add stacking-energies using base pair adjacencies. Comparison tests were performed against the original serial GA on known structures that are(More)
This work builds on previous research from an EA used to predict secondary structure of RNA molecules. The EA has the goal of predicting which canonical base pairs will form hydrogen bonds and helices. The addition of stacking energies, through INN and INN-HB, to our thermodynamic model has enhanced our predictions. We test three RNA sequences of lengths(More)
This paper presents a fully parallel version of RnaPredict, a genetic algorithm (GA) for RNA secondary structure prediction. The research presented here builds on previous work and examines the impact of three different pseudorandom number generators (PRNGs) on the GA's performance. The three generators tested are the C standard library PRNG RAND, a(More)
Two extensive analyzes on RnaPredict, an evolutionary algorithm for RNA folding, are presented here. The first study evaluates the performance of individual nearest neighbor (INN) and individual nearest neighbor-hydrogen bond (INN-HB), two stacking-energy thermodynamic models; the criteria for comparison is the correlation between the prediction accuracy(More)
This paper presents a parallel version of <i>RnaPredict</i>, a genetic algorithm (GA) for RNA secondary structure prediction. The research presented here builds on previous work and examines the impact of three different pseudorandom number generators (PRNGs) on the GA's performance. The three generators tested are the C standard library PRNG RAND, a(More)
We report the further application of a novel approach to template and ligand design by the synthesis of agonists of the melanocortin receptor. This design method uses the conserved structural data from the three-dimensional conformations of beta-turn peptides to design rigid nonpeptide templates that mimic the orientation of the main chain C-alpha atoms in(More)