Universitat Internacional de Catalunya

Structural Bioinformatics

Structural Bioinformatics
5
14524
4
First semester
op
MENTION IN BIOINFORMATICS
Main language of instruction: English

Other languages of instruction: Catalan, Spanish

Teaching staff


Dr. DE LA CRUZ MONTSERRAT, Francisco Javier - xdelacruz@uic.es

Doubts will be addressed before or after class. Non-face-to-face doubts will be addressed by videoconference.

Introduction

This course provides the fundamental concepts for using structural information in biomedical/clinical problems. In particular, we will address the fundamental relationship between structure and function, analyzing the three-dimensional structures of proteins, DNA and RNA. We will see how to graphically and automatically process the three-dimensional structures of macromolecules. Subsequently, we will see the different methodologies available to generate structural information using cutting-edge techniques, including Artificial Intelligence algorithms. Finally, we will see how to use structural bioinformatics to address biomedical problems related to the molecular understanding of hereditary disease.  

Pre-course requirements

It is recommended to have completed and passed:

Introduction to Bioinformatics

Biomolecular Interactions

Objectives

- Understand how the relationship between structure and function is the basis for the application of structural bioinformatics methods in biomedicine 
- Know how to generate structural information: difference between extraction and prediction 
- Use structural information to analyze genetic information and solve associated biomedical/clinical problems

Competences/Learning outcomes of the degree programme

CB3 Students will gain the ability to gather and interpret relevant data (normally within their area of study) to make judgments that include a discussion on relevant issues of a social, scientific or ethical nature

CG7 Integrate the basic concepts related to the field of biomedicine both at theoretical and experimental levels.

CG10 Design, write and execute projects related to the area of Biomedical Sciences

CG11 Recognize basic concepts of different areas related to biomedical sciences.

CT5 Use the Internet as a way of communication and as a source of information.

CT6 Know how to communicate, make presentations and write scientific papers.

CT7 Be able to work in a team.

Learning outcomes of the subject

Understand the aspects that require the use of structural information in biomedical problems. Learn how to obtain the structural information of interest by applying techniques from the field of structural bioinformatics, such as the extraction of structural information, molecular modeling/prediction, database management, etc. Apply knowledge to understand the molecular basis of hereditary diseases and predict genetic variants' pathogenicity.

Syllabus

A. STRUCTURE: THE LOCUS OF FUNCTION 

1) PRINCIPLES OF STRUCTURAL BIOLOGY.

1.1 Function at the sequence level. 

1.2 The structure of macromolecules. 

1.3 From structure to function. 

1.4 Stability: a key concept for protein structure and function. 

 

B. USING BIOINFORMATICS TO GENERATE STRUCTURAL INFORMATION

2) EXTRACTING INFORMATION FROM STRUCTURE 

2.1 Visual exploration of structures. 

2.2 Computational analysis: generalizing visual exploration. 

 

3) GENERATING STRUCTURAL INFORMATION: STRUCTURE PREDICTION. Instructors. X. de la Cruz, S. Özkan. 12h

3.1 From sequence to structure: a key problem. 

3.2 Homology/comparative modeling. 

3.3 Disorder predictions.  

3.4 De novo structure prediction. AlphaFold: the new paradigm. 

4) GENOME STRUCTURAL ANALYSIS. 

5) RNA STRUCTURE PREDICTION. 

6) BEYOND STRUCTURE: UNDERSTANDING AND COMPUTING MACROMOLECULAR FLEXIBILITY. 

7) STRUCTURE IN SYSTEMS BIOLOGY. 


C) APPLYING STRUCTURAL BIOINFORMATICS IN BIOMEDICINE

8) UNDERSTANDING THE MOLECULAR BASIS OF GENETIC DISEASE. 

Teaching and learning activities

In person



Lectures: 50 minutes presentation of a theoretical topic by the teacher.  Case Methods (CM): Explanation and discussion of a real or imaginary situation/case. The students work on the questions formulated together with the instructor and the answers are discussed. The instructor actively intervenes and, if necessary, contributes new knowledge.

Evaluation systems and criteria

In person



First call students:  Case methods: 25%  Partial exam: 35%  Final exam: 40% 
Students in second or subsequent call:  The grade of the methods of the case will be saved; and the final exam will represent 75% of the final grade. Repeating students who wish to repeat the partial in 3 or 5 calls, may do so by previously communicating it to the head teacher. 
Geineral points to keep in mind about the evaluation system:  1) To be able to do average, in the final exam a minimum grade of 5 must be obtained.  2) In adition to (1), to pass the subject the average of all the evaluations items must be 5 or more. 3) The continuous nature of this evaluation system means that it is not possible to evaluate the subject if you have not participated in a minimum of 75% of the hours.  4) The improper use of electronic devices (such as the recording and broadcasting of both students and teachers during the different lessons, as well as the use of these devices for recreational and non-educational purposes) may lead to expulsion from class.

Evaluation period

E: exam date | R: revision date | 1: first session | 2: second session:
  • E1 16/01/2023 I1 16:00h
  • E2 22/06/2023 A04 18:00h
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