Bioinformatics

Code:

Q4025

Acronym:

Q4025

Level:

400

Keywords
Classification	Keyword
OFICIAL	Chemistry

Instance: 2020/2021 - 2S

Active?	Yes
Responsible unit:	Department of Chemistry and Biochemistry
Course/CS Responsible:	Master in Biochemistry

Cycles of Study/Courses

Acronym	No. of Students	Study Plan	Curricular Years	Credits UCN	Credits ECTS	Contact hours	Total Time
M:BQ	6	Plano de Estudos do MBIOQ_2013-2014	1	-	6	56	162
M:Q	6	Official study plan until 2022/2023	1	-	6	56	162

Teaching language

Portuguese
Obs.: A língua de ensino será o Português se todos os estudantes pertencerem a países de língua oficial portuguesa. Caso contrário, a língua de ensino será o Inglês.

Objectives

The main objective of the lectures is to provide a broad overview of Molecular Bioinformatics.
In the practical classes the students will develop small research projects.

Learning outcomes and competences

Expertise in the use of molecular bioinformatic tools and software. Capacity to identify bioactive compounds by virtual screening. Expertise in macromolecule modelling. Expertise in computational (bio)chemical reactivity. Capacity for choosing the most adequate bioinformatic tool for each biochemical problem.

 

Working method

Presencial

Program

Lectures.

1. Protein structure and modelling.
2. Homology Modelling.
3. Docking protein-ligand.
4. Virtual Screening
5. Electronic Scructure and enzymatic reactivity. 


Practical classes.

The students will develop small research projects in the fields covered by the lectures.

Mandatory literature

Leach Andrew R.; Molecular modelling. ISBN: 0-582-38210-6
Sousa, S. F., Ribeiro, A. J. M., Neves, R. P. P., Bras, N. F., Cerqueira, N., Fernandes, P. A., & Ramos, M. J.; Application of quantum mechanics/molecular mechanics methods in the study of enzymatic reaction mechanisms, Wiley Interdisciplinary Reviews-Computational Molecular Science, 7(2). doi:10.1002/wcms.1281, 2017
Simoes, I. C. M., Costa, I. P. D., Coimbra, J. T. S., Ramos, M. J., & Fernandes, P. A.; New Parameters for Higher Accuracy in the Computation of Binding Free Energy Differences upon Alanine Scanning Mutagenesis on Protein-Protein Interfaces, Journal of Chemical Information and Modeling, 57(1), 60-72. doi:10.1021/acs.jcim.6b00378
Cerqueira, N., Gesto, D., Oliveira, E. F., Santos-Martins, D., Bras, N. F., Sousa, S. F., Fernandes P. A., Ramos, M. J.; Receptor-based virtual screening protocol for drug discovery, Archives of Biochemistry and Biophysics, 582, 56-67. doi:10.1016/j.abb.2015.05.011
João Marques Sousa, Matilde Ribeiro Viegas, Pedro Teixeira Ferreira, Pedro Coelho Paiva, Ana Luísa Oliveira, Pedro Alexandrino Fernandes, Maria João Ramos; Bioinformática Molecular, Faculdade de Ciências, Universidade do Porto, 2020

Teaching methods and learning activities

Lectures, often realised with workshops.
Practical computational classes, with one student per computer.

Evaluation Type

Distributed evaluation with final exam

Assessment Components

designation	Weight (%)
Apresentação/discussão de um trabalho científico	10,00
Trabalho escrito	75,00
Trabalho prático ou de projeto	15,00
Total:	100,00

Amount of time allocated to each course unit

designation	Time (hours)
Estudo autónomo	30,00
Frequência das aulas	40,00
Trabalho escrito	30,00
Total:	100,00

Eligibility for exams

Attendance of 75% of the practical classes, presentationof a written report (75%) of the work done in the practical classes, and oral team presentation (10%) of a small scientific individually written work (15%).

Calculation formula of final grade

The final grade of the discipline of Molecular Bioinformatics I consists on the sum of:

- the grade obtained in the labs and the corresponding report made by the student, individually, with no more than 7500 words (75% of the final grade);

- the grade obtained in an individual written work, in the form of an article, on virtual screening, with no more than 2500 words (15% of the final grade);

- the grade obtained in a team oral presentation, on virtual screening (10% of the final grade).

Classification improvement

Oral session on the theory given during the course and the practical work carried out during the course.