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Parallel Implementation of the Branch and Bound Method in the Protein Folding Problem

Student: Iaroslav Abramov

Supervisor: Mikhail Posypkin

Faculty: HSE Tikhonov Moscow Institute of Electronics and Mathematics (MIEM HSE)

Educational Programme: Supercomputer Modeling in Science and Engineering (Master)

Final Grade: 7

Year of Graduation: 2020

The functions of a protein are determined by its native structure. Amongthe various models describing this process, the Hydrophobic-Polar(HP) modelaccurately enough simplifies protein folding process and allows us to reduce acomplicity of predicting the real conformation. A lot of methods of global optimizationare able to use in HP folding model. In this study, branch and bound method andthe ion motion algorithm(IMO) method was implemented to the HP model forthe protein folding prediction. These methods was improved by additional data -management, greedy modification and parallel calculations. That gains superiorefficiency over under watched methods.

Full text (added May 20, 2020)

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