Molecular Bioinformatics

Code:

Q4100

Acronym:

Q4100

Level:

400

Keywords
Classification	Keyword
OFICIAL	Chemistry

Instance: 2021/2022 - 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	1	PE_Bioinformatics and Computational Biology	1	-	6	42	162
M:BBC	9	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
Apresentação/discussão de um trabalho científico	25,00
Participação presencial	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 and oral presentation of the research work carried out.

Calculation formula of final grade

The final mark corresponds to the average of the mark obtained in the exam and the mark given in the practical classes and corresponding report made by the student.

The mark obtained in the exam mostly reflects the result of the final exam, which is scheduled by the Conselho Pedagógico of the Faculty. The weight of the exam for the final mark is 50%.

The practical mark is the result of the continuous evaluation during the practical classes (15% of the final mark),  the oral presentation (10% of the final mark) and report (25% of the final mark) of the research work carried out. in the practical classes.

Examinations or Special Assignments

Oral presentationt on the work carried out in the practical classes.

Classification improvement

Repeating the final exam.