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Computational Biochemistry

Code:

BINF026

Sigla:

BC

Áreas Científicas
Classificação	Área Científica
OFICIAL	Biotecnologia

Ocorrência: 2023/2024 - 1S

Ativa?	Yes
Página Web:	https://moodle.ips.pt/2324/course/view.php?id=547
Unidade Responsável:	Departamento de Engenharia Química e Biológica
Curso/CE Responsável:	Undergraduate in Bioinformatics

Ciclos de Estudo/Cursos

Sigla	Nº de Estudantes	Plano de Estudos	Anos Curriculares	Créditos UCN	Créditos ECTS	Horas de Contacto	Horas Totais
BINF	17	Study Plan	3	-	5	52,5	148,5

Língua de trabalho

Portuguese

Objetivos

skills, focusing on structure modelling, protein modelling and protein interactions. Students will learn the validity
and applicability of molecular dynamics methods applied to biomolecular problemas – proteins, nucleic acid, and membranes.

Using the contents of this curricular unit students will be able to:
-Choose the appropriate technique to model problems relating to structural;
-Set-up and run the necessary calculations;
-Use the existing analysis tools or write their own, using the programming skills from previous UCs.

Students will learn the fundamental skills of structure simulation, with some exercise classes focused on learning
the details.

Resultados de aprendizagem e competências

-

Modo de trabalho

Presencial

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

This UC requires the capacity to write scripts, in any programming language but preferentially in Phyton, and analytical geometry skills, not covered in the UC; it also mobilizes Organic Chemistry and Biochemistry knowledge.

Programa

1. Introduction – atomic and molecular structure; bonds and interactions; general view of methods – classical, semi-empirical, DFT and ab initio – characteristics, applicability and limits. Force fields, thermostats, and barostats. Molecular dynamic best pratices.

2. Structure of proteins and nucleic acids – revision. Contribution of non covalent interactions for the structure and function of proteins and nucleic acids.

3. Modelling proteins and nucleic acids – molecular mechanics and dynamics applied to proteins; forcefields, application and limits.

4. Lipids and membranes – a molecular dynamics approach. Simulation of transmembrane proteins.

5. Protein-ligand interactions – docking, applicability and limits; post-docking analysis -molecular dynamics-based refining.

6. Protein interaction – the interactome; protein-protein docking tools.

Bibliografia Obrigatória

Bruce Alberts; Molecular Biology of the Cell, Garland Science, 2014. ISBN: 978-0815344643
Frank Jensen; Introduction to Computational Chemistry, Wiley, 2017. ISBN: 978-1118825990
Harvey Lodish, Arnold Berk, S Lawrence Zipursky, Paul Matsudaira, David Baltimore, and James Darnell; Molecular Cell Biology, WH Freeman, 2000. ISBN: 0-7167-3136-3
Atkins, Keeler, de Paula; Atkins' Physical Chemistry, Oxford University Press. ISBN: 9780198769866
Introduction to Computational Chemistry; GROMACS 2021.4 Manual (2021.4), 2021

Métodos de ensino e atividades de aprendizagem

Per week: 60 minutos T classes, describing theory and techniques, plus 120 minutes of hand-on computational classes for different simulation techniques focused on solving exercises, software use, work planning and result interepretation.

Software

AutoDock Vina - https://vina.scripps.edu/
GROningen MAchine for Chemical Simulations (GROMACS) - https://www.gromacs.org/
Visual Molecular Dynamics (VMD) - https://www.ks.uiuc.edu/Research/vmd/

Tipo de avaliação

Distributed evaluation with final exam

Componentes de Avaliação

Designation	Peso (%)
Teste	40,00
Trabalho laboratorial	60,00
Total:	100,00

Componentes de Ocupação

Designation	Tempo (Horas)
Frequência das aulas	45,00
Estudo autónomo	65,00
Trabalho de investigação	25,00
Total:	135,00

Obtenção de frequência

Not applicable.

Fórmula de cálculo da classificação final

Continuous Assessment:

FC= 60% (average of 12 work) + 40% Test
Minimum classification of 6 in test.

Exam:

FC= 100 % Exam

Provas e trabalhos especiais

Continuous evaluation - 12 works wirh delivery spread over the semester (laboratory works), 3 tests about T classes and the lab works (L classes).

Trabalho de estágio/projeto

Not applicable.

Melhoria de classificação

By exam only. No previous evaluation items are considerable.