Biophysics and structural bioinformatics I

Course content

This course is divided into two parts.

Part I: biophysics

- Introduction to the structure of proteins, DNA and RNA.

- Introduction to the experimental determination of protein structures.

- Thermodynamics and kinetics of protein folding.

- Protein folding: identification of intermediates and transition states.

- Description of intra- and inter-molecular interactions in biomolecules.

- Structural aspects of protein-DNA interactions.

Part II: bioinformatics

- Methods of alignment / superimposition of protein structures.

- Energy functions.

- Prediction of the secondary structure of proteins

- Prediction of the 3D structure of proteins: comparative modeling, fold recognition, ab initio methods

- Structural characteristics of proteins involved in conformational diseases (Creutzfeld-Jakob disease,Alzheimer's, ...).

- Membrane proteins.

Objectives (and/or specific learning outcomes)

At the end of the course, the student will be able:

To share a common vocabulary with experimentalists in structural biology.
To evaluate the quality and the reliability of experimentally resolved structures of biomolecules.
To explain the general bases in the field of structural bioinformatics.
To demonstrate in his explanation his deep understanding of the concepts.
To apply a scientific approach in the choice of a bioinformatics tool to find an answer to a problem.
To demonstrate critical thinking in analyzing the results of bioinformatics tools.

Teaching methods and learning activities

Theoretical courses, remote teaching through videos and practicals on computers

Contribution to the teaching profile

1.1. Acquire the concepts and fundamental knowledge of computer science and biology necessary for the development of bioinformatics or modeling projects.

1.4. Master the mathematical, statistical and computational approaches on which bioinformatics and modeling studies are based.

1.5. Be able to use existing bioinformatics resources and develop new software (algorithms, databases, analysis tools, etc.)..

3.1. Understand abstraction and its role in the development of a theory or model.

References, bibliography, and recommended reading

(non exhaustive) Protein Physics, A.V. Finkelstein & O.B. Ptitsyn, Academic Press (2002); Protein Folding Mechanisms, Advances in Protein Chemistry, Vol 53, edt by C.R. Matthews, Academic Press (2000); Biophysique moléculaire, M. Daume, InterEditions, Paris, 1993.

Course notes

Podcast
Université virtuelle

Other information

Contacts

Email: dimitri.gilis@ulb.be and marianne.rooman@ulb.be

Office : Solbosch, UD3.203 et UD3.204

Phone: 02 650 36 15 and 02 650 20 67

Campus

Solbosch

Evaluation

Method(s) of evaluation

Oral examination
Written report

Oral examination

Written report

For the practical part, the last session corresponds to a synthesis of what has been achieved during the year. An individual report must be submitted for this session and will be used for the evaluation of the practical part. Any student who does not submit his or her report for the practicals will not be allowed to take the oral exam.

The "theory" part of the course is assessed by an oral examination, lasting 25 minutes, without preparation. Two questions will be selected at random by the student. Both questions will be discussed in relation to the whole course.

Mark calculation method (including weighting of intermediary marks)

Let nE be the mark of the oral exam and nR be the mark of the report of the practicals. The final mark, nF, is calculated by the following method:

if (nE < 7/20 AND nR < 7/20) OR (nE >= 7/20 AND nR >= 7/20), then nF = nR*0,2 + nE*0,8
in the other cases : nF = min(nR , nE)

If nR < 10/20 and the teaching unit has not been credited at the end of the first session, a new report must be submitted in the second session. On the other hand, if nR >= 10/20, the mark is carried over from one session to the next.

If a student does not submit its report for the practicals or does not attend the examination, the final mark is a mark of absence.

Carry over of the mark obtained for the report of the practicals from one academic year to the next

If a student has not been credited for the BINF-F403 teaching unit but has obtained a mark of 10/20 or higher for the practicas, this will be carried over and the student will be exempt from the practicals, unless he/she requests otherwise.

Language(s) of evaluation

french
english