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Computational Biochemistry

Code:

BINF026

Sigla:

BC

Áreas Científicas
Classificação	Área Científica
OFICIAL	Biotecnologia

Ocorrência: 2020/2021 - 1S

Ativa?	Yes
Página Web:	https://moodle.ips.pt/2021/course/view.php?id=2090
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	13	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)

Not applicable

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

Cramer, C.J; Essentials of Computational Chemistry: Theories and Models. ISBN: N 978-0-470-09182-1.
Tsai, C.S; An Introduction to Computational Biochemistry. ISBN: 978-0-471-40120-9
Kukol, A.; Molecular Modeling of Proteins. ISBN: 978-1-58829-864-5

Métodos de ensino e atividades de aprendizagem

Theoretical classes will be dedicated to exposing the themes of the UC program and introducing practical work. The Pratical-laboratoy classes will be held on computers, where work will be carried out on the simulation of biological systems in the context of computational biochemistry, as well as the analysis and interpretation of results.

Software

GROMACS
qtgrace
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	52,50
Estudo autónomo	66,00
Trabalho laboratorial	30,00
Total:	148,50

Obtenção de frequência

Not applicable

Fórmula de cálculo da classificação final

Continuous accessment:
Final grade = 0.40 * (average grade of 2 tests) + 0.60 * (average grade of 2 questionaries of the pratical works) 
Evaluation by Exam:
Final grade = 100% exame grade