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Modelling Techniques Applyed to Biotechnology

Code:

MEBQB09

Sigla:

TMAB

Áreas Científicas
Classificação	Área Científica
OFICIAL	Biotecnologia

Ocorrência: 2021/2022 - 2S

Ativa?	Yes
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	1	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.

In addition, students must also acquire skills in network / metabolic path modeling techniques, as an approach to the study of the effect of manipulating protein expression in model systems.

 

Resultados de aprendizagem e competências

Non applicable

Modo de trabalho

Presencial

Pré-requisitos (conhecimentos prévios) e co-requisitos (conhecimentos simultâneos)

Non applicable

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. Use of simulation software: NWChem, MOPAC, GROMACS; molecular publishers and accessory programs for visualization and analysis.
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. Use of simulation software: PLAS or SBW; data processing software.

Bibliografia Obrigatória

Cramer, C.J.; Essentials of Computational Chemistry: Theories and Models, wiley. ISBN: ISBN 978-0-470-09182-1
Jensen, F.; Introduction to Computational Chemistry, wiley. ISBN: ISBN 978-0-470-01186-7
Rogers, D.W.; Computational Chemistry Using the PC, Wiley-Interscience. ISBN: 978-0-471-42800-8
Tsai, C.S.; An Introduction to Computational Biochemistry, Wiley-Liss. ISBN: ISBN 978-0-471-40120-9
Xu, Y., Xu, D., Liang, D.; Computational Methods for Protein Structure Prediction and Modeling, Springer. ISBN: ISBN 978-0-387-68372-0 (vol. 1)
Xu, Y., Xu, D., Liang, D.; Computational Methods for Protein Structure Prediction and Modeling, Springer. ISBN: ISBN 978-1-4419-2206-9 (vol. 2).
Fell, D; Understanding the Control of Metabolism (Frontiers in Metabolism), Portland Press. ISBN: ISBN 978-1-855-78047-7
Bower, J.M., Bolouri, H. ; Computational Modeling of Genetic and Biochemical Networks, Bradford Book. ISBN: ISBN 978-0-262-52423-0
Britton, N.F; Essential Mathematical Biology, Springer. ISBN: ISBN 978-1-852-33536-6
Heinrich, R., Schuster, S.; The Regulation of Cellular Systems, Springer. ISBN: 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.

Continuous Evaluation:
2 computational works, each with a 50% weight. In each work, the lab/computational performance and the written report have, each, a 50% weight.

1st / 2nd Season Evaluation and Special Season: 100% Exam.


If it is not possible to carry out the test / examination in person, due to the SARS-CoV-2 pandemic, teachers may require students to carry out an oral test  for all students who have obtained a rating greater than or equal to 9.5. The final grade in the course will be the grade obtained in the oral exam.

Software

PLAS
VMD
COPASI
GROMACS

Tipo de avaliação

Distributed evaluation with final exam

Componentes de Avaliação

Designation	Peso (%)
Trabalho escrito	50,00
Trabalho laboratorial	50,00
Total:	100,00

Componentes de Ocupação

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

Obtenção de frequência

Non applicable

Fórmula de cálculo da classificação final

Continuous Evaluation:
0.5 * work 1 grade + 0.5 * work 2 grade

1st / 2nd Season Evaluation: 100% Exam.