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Computational Biochemistry

Code:

BINF026

Sigla:

BC

Áreas Científicas
Classificação	Área Científica
OFICIAL	Biotecnologia

Ocorrência: 2021/2022 - 1S

Ativa?	Yes
Página Web:	https://moodle.ips.pt/2122/course/view.php?id=1738
Unidade Responsável:	Biotecnologia
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	26	Study Plan	3	-	5,5	60	148,5

Língua de trabalho

Portuguese

Objetivos

The UC aims to develop chemical and biochemical structure-based computational skills, focusing on structure modelling, protein modelling and protein interactions. Students will learn the validity and applicability of semi-empirical, density functional theory and ab initio methods, as well as the basics of molecular mechanics and dynamics and of protein-ligand and protein-protein docking.

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; Schrödinger’s equation and its application on computational chemistry and biochemistry. Software for drawing and visualization; software packages.

2. Computational chemistry – semi-empirical methods, density functional theory and ab initio methods; characteristics, applications and limitations

3. Computational chemistry – implicit and explicit models for condensed phases

4. Protein modeling – homology and ab initio approaches to protein structure

5. Protein modeling – molecular mechanics and dynamics approaches to biological questions; force fields, their applicability and limitations

6. Lipids and membranes - computational approaches to modelling

7. Protein-ligand interactions – docking techniques, applications and limitations; post-docking analysis – quantum chemistry and molecular mechanics/dynamics based refinements

8. Protein-protein interactions – the interactome; tools for protein-protein docking.

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: 90 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	45,00
Trabalho laboratorial	55,00
Total:	100,00

Componentes de Ocupação

Designation	Tempo (Horas)
Frequência das aulas	52,50
Estudo autónomo	50,00
Trabalho de investigação	20,00
Trabalho escrito	26,00
Total:	148,50

Obtenção de frequência

Not applicable.

Fórmula de cálculo da classificação final

Continuous Assessment:

FC= 45% (average of 2 tests) + 55% (average of 5 lab reports grades)

Exam:

FC= 100 % Exam

Provas e trabalhos especiais

Continuous evaluation - 2 tests about T classes; 5 lab works (L classes) with reports about each work to be turned in by the students.

Trabalho de estágio/projeto

Not applicable.

Avaliação especial (TE, DA, ...)

Working students - tests will be performed as usual, in class; lab classes reports can be turned in until the last day of classes of the semester.

Students in virtual mobility - tests will be made available online so students can answer them as if they were in class.

Melhoria de classificação

By exam only. No previous evaluation items are considerable.