Abu Zafer M. Dayem Ullah

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BACKGROUND The protein folding problem remains one of the most challenging open problems in computational biology. Simplified models in terms of lattice structure and energy function have been proposed to ease the computational hardness of this optimization problem. Heuristic search algorithms and constraint programming are two common techniques to approach(More)
Over the past few years, several local search algorithms have been proposed for various problems related to multicast routing in the off-line mode. We describe a population-based search algorithm for cost minimisation of multicast routing. The algorithm utilises the partially mixed crossover operation (PMX) under the elitist model: for each element of the(More)
In the present study, we define derivative scoring functions from PITA and STarMir predictions. The scoring functions are evaluated for up to five selected miRNAs with a relatively large number of validated targets reported by TarBase and miRecords. The average ranking of validated targets returned by PITA and STarMir is compared to the average ranking(More)
Ab initio protein folding simulation largely depends on knowledge-based energy functions that are derived from known protein structures using statistical methods. These knowledge-based energy functions provide us with a good approximation of real protein energetics. However, these energy functions are not very informative for search algorithms and fail to(More)
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