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Protein docking GPU acceleration
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| 5.13 MB | Adobe PDF |
Orientador(es)
Resumo(s)
In Bioinformatics, finding the complex resulting from an interaction between a pair of
proteins is a computationally demanding task. There are methods and algorithms that
simulate the binding between two proteins. However, the computation related to docking
simulation has many extensive and repeating steps. Thus, the execution of the simulation
if the program is CPU-only can last for hours, making the option of using these programs
a very inefficient one in terms of work/time.
One of the methods used is BiGGER, created by prof. Nuno Palma and others. This
algorithm has features that give it a lower time complexity compared to others, therefore
execution times in BiGGER can be lower than most of the algorithms fitted for execution
of docking simulations. Studying protein interactions has medical aplications, contributing
to the development of ways to protect, diagnose and heal humanity from neuronal
diseases. It also contributes to computer assisted drug design and development. To improve
the execution time of docking programs, these were optimized for GPU execution,
reducing the execution time in docking scenarios that can last for hours to minutes or
even seconds.
This document presents an aproach to the implementation of optimizations to BiGGER,
running it with GPU assistance. This implementation is to be done via high performance
computing techniques, so that the machine’s GPU assists the CPU on parallelizing
those required computations. By having more resources at disposal, it should be expected
that the execution time of BiGGER is reduced due to the improvement of BiGGER
performance in relation to the sequential version.
If the implementations succeed, there will be additional advantages for BiGGER in
relation to other algorithms. Thus, a value proposition is given for those who intend
to use BiGGER as a method for efficiently studying interactions between proteins in a
personal ou professional computer.
Descrição
Palavras-chave
proteins docking high performance computing GPU Bioinformatics BiGGER