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Modelling Techniques Applyed to Biotechnology

Code:

MEBQB09

Sigla:

TMAB

Áreas Científicas
Classificação	Área Científica
OFICIAL	Biotecnologia

Ocorrência: 2019/2020 - 2S

Ativa?	Yes
Página Web:	https://www.estbarreiro.ips.pt/files/1A2S_PB_T%C3%A9cnicas%20de%20Modela%C3%A7%C3%A3o%20Aplicadas%20%C3%A0%20BT.pdf
Unidade Responsável:	Biotecnologia
Curso/CE Responsável:	Master in Biological and Chemical Engineering

Ciclos de Estudo/Cursos

Sigla	Nº de Estudantes	Plano de Estudos	Anos Curriculares	Créditos UCN	Créditos ECTS	Horas de Contacto	Horas Totais
MEBQ	17	Study Plan	1	-	5	45	135

Língua de trabalho

Portuguese

Objetivos

At the end of the semester, it is expected that students understand and are able to apply some of the
techniques of modelling structure of molecules relevant in the context of biotechnological
applications - modelling and optimization of structures of small molecules, proteins and lipid
structures.

Resultados de aprendizagem e competências

At the end of the semester, it is expected that students understand and are able to apply some of the
techniques of modelling structure of molecules relevant in the context of biotechnological
applications - modelling and optimization of structures of small molecules, proteins and lipid
structures.

Modo de trabalho

À distância

Programa

1. Methods of Molecular Modelling: Principles of computational chemistry applied to optimize
structures of small molecules; principles of molecular mechanics and dynamics; docking of ligands
to proteins. Obtaining structures. Modelling of small molecules - study of potential ligands as
potential modulators of protein activity; application of molecular modelling for structural
resolution - mass spectrometry and NMR. Chemical applications of molecular modelling. Study of
the interaction by docking of ligands to proteins.

2. Metabolic Modelling: Methodologies for building models - law of mass action and power laws.
Numerical and symbolic analysis of FDE's and ODEs. Stoichiometric and sensitivity analysis.

Bibliografia Obrigatória

Lindahl; Abraham; Hess; van der Spoel; GROMACS 2020.2 Manual (https://doi.org/10.5281/zenodo.3773799)

Bibliografia Complementar

Cramer, C.J.; Essentials of Computational Chemistry: Theories and Models. ISBN: 978-0-470- 09182-1.
Jensen, F; Introduction to Computational Chemistry. ISBN: 978-0-470-01186-7
Tsai, C.S.; An Introduction to Computational Biochemistry. ISBN: 978-0-471-40120-9
Rogers, D.W.; Computational Chemistry Using the PC. ISBN: 978-0-471-42800-8
Xu, Y., Xu, D., Liang, D.; Computational Methods for Protein Structure Prediction and Modeling
Fell, D.; Understanding the Control of Metabolism (Frontiers in Metabolism). ISBN: 978-1-855-78047-7
Bower, J.M., Bolouri, H.; Computational Modeling of Genetic and Biochemical Networks. ISBN: 978-0-262-52423-0
Britton, N.F.; Essential Mathematical Biology. ISBN: 978-1-852-33536-6
Heinrich, R., Schuster, S.; The Regulation of Cellular Systems. ISBN: 978-0-412-03261-5

Métodos de ensino e atividades de aprendizagem

This curricular unit comprises a theoretical / practical component, in which the contents are taught
via a computer readable presentations of PowerPoint. The practical component includes classes in a
computer lab, to perform small projects on the mentioned software in the syllabus.

Remote teaching -
Theory-focused classes - replaced with autonomous work; the teacher will provide reading material in one week that will be evaluated in the next using quizzes.
Practical classes - assuming adequate computing resources are available to students - small and detailed protocols wihh be available weekly to be executed by the students, effectively breaking out the larger intented work in small parts; evaluation will be based on the work results obtained by the students using quizzes.

Software

VMD
GROMACS
qtGrace/grace/xmgrace
PLAS

Tipo de avaliação

Distributed evaluation with final exam

Componentes de Avaliação

Designation	Peso (%)
Teste	30,00
Trabalho laboratorial	40,00
Trabalho escrito	30,00
Total:	100,00

Componentes de Ocupação

Designation	Tempo (Horas)
Estudo autónomo	90,00
Frequência das aulas	45,00
Total:	135,00

Obtenção de frequência

Not applicable.

Fórmula de cálculo da classificação final

Continuous evaluation - Unweigthed arithmetic average of the classifications of all work elements throughout the semestre.
Evaluation by final examination - 100% exam note.