Molecular Bioinformatics

Code:

Q4100

Acronym:

Q4100

Level:

400

Keywords
Classification	Keyword
OFICIAL	Chemistry

Instance: 2022/2023 - 2S

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

Cycles of Study/Courses

Acronym	No. of Students	Study Plan	Curricular Years	Credits UCN	Credits ECTS	Contact hours	Total Time
E:BBC	0	PE_Bioinformatics and Computational Biology	1	-	6	42	162
M:BBC	12	The study plan since 2018	1	-	6	42	162

Teaching language

Suitable for English-speaking students

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. Molecular mechanics.
3. Docking protein-ligand.
4. Virtual Screening
5. Computational mutagenesis.
6. 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

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 (%)
Exame	50,00
Participação presencial	25,00
Trabalho prático ou de projeto	25,00
Total:	100,00

Amount of time allocated to each course unit

designation	Time (hours)
Elaboração de relatório/dissertação/tese	24,00
Estudo autónomo	70,00
Frequência das aulas	56,00
Total:	150,00

Eligibility for exams

Attendance of 75% of the practical classes.

Calculation formula of final grade

The Final Grade of the Molecular Bioinformatics course consists of the average of the sum of the grade obtained in the final exam and the grade obtained in practical classes and the corresponding report made by the student.



Theoretical Grade

The theoretical grade is given by the grade of the final theoretical exam whose date is set by the Pedagogical Council of the F.C.U.P. Its value is 50% of the final grade.



Practical Grade

The practical grade corresponds to the continuous assessment (25% of the final grade) and report (25% of the final grade) of the research work carried out in practical classes. Its value is 50% of the final grade.

Classification improvement

Repeating the final exam.