Estudio del problema del plegado de proteínas
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2024
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Abstract
En este trabajo se trata el problema del plegado de proteínas, uno de los problemas más importantes de la bioinformática. Esta disciplina estudia la aplicación de tecnologías informáticas, estadísticas y matemáticas para la resolución de problemas abiertos en biología. A lo largo del texto se estudiarán distintos modelos matemáticos propuestos en base a su complejidad y aproximabilidad. Se darán en primer lugar nociones básicas sobre estas ramas de las ciencias de la computación y las distintas clases en las que se pueden agrupar los problemas informáticos. Tras esto se explicarán las demos tracciones existentes para los modelos recogidos, sirviendo para aunar conocimiento diverso sobre la materia. Adicionalmente, se hablará de un nuevo modelo propuesto originalmente en este trabajo teniendo en cuenta las propiedades bioquímicas de las proteínas. El nuevo modelo está creado en colaboración con estudiantes de bioquímica que nos han asesorado para asegurar la corrección del mismo. La segunda parte del trabajo se centrará en poner a prueba los algoritmos pro puestos e implementados, comparando su eficiencia en cada caso para distintos modelos y en contraposición a otras formas de resolución de algoritmos de optimización como los algoritmos bioinspirados.
In this work we cover the protein folding problem, one of the most important problems in bioinformatics. This discipline studies the application of computer tech nologies, statistics and mathematics to the resolution of open problems in biology. Throughout this text several mathematical models will be studied according to their complexity and approximability. Firstly, we will introduce some basic notions about these areas in computer science and the different classes in which we can group informatic problems. After this we will explain existing demonstrations for the treated problems in order to unite diverse knowledge about this matter. Addi tionally, we will propose an original new model taking the biochemical properties of proteins into account. This model is created in collaboration with biochemistry students who have helped us to assure its correction. The second part of the work will focus on testing the proposed and implemented algorithms to check their efficiency for different models and test them against other forms of resolution for optimization problems such as bioinspired algorithms.
In this work we cover the protein folding problem, one of the most important problems in bioinformatics. This discipline studies the application of computer tech nologies, statistics and mathematics to the resolution of open problems in biology. Throughout this text several mathematical models will be studied according to their complexity and approximability. Firstly, we will introduce some basic notions about these areas in computer science and the different classes in which we can group informatic problems. After this we will explain existing demonstrations for the treated problems in order to unite diverse knowledge about this matter. Addi tionally, we will propose an original new model taking the biochemical properties of proteins into account. This model is created in collaboration with biochemistry students who have helped us to assure its correction. The second part of the work will focus on testing the proposed and implemented algorithms to check their efficiency for different models and test them against other forms of resolution for optimization problems such as bioinspired algorithms.
Description
Trabajo de Fin de Grado del Doble Grado en Ingeniería Informática y Matemáticas, Facultad de Informática UCM, Departamento de Sistemas Informáticos y Computación, Curso 2023/2024.
Información adicional del algoritmo en GitHub:
https://github.com/Javi153/TFG/tree/main/Codigo/Algoritmo%20genetico%20HP
https://github.com/Javi153/TFG/tree/main/Codigo/Algoritmo%20aproximacion%20HP
https://github.com/Javi153/TFG/tree/main/Codigo/Algoritmo%20aproximacion%20HPNX