Biomolecular Simulation


The knowledge and skills acquired in this curricular unit will allow the students to have a general understanding of the scientific literature in the area, to use general software tools to tackling scientific problems involving structural bioinformatics, and, by (individually) deepening their knowledge on selected areas, to start supervised research projects in these areas of work to study real-life problems in biosciences.

General characterization





Responsible teacher

João Montargil Aires de Sousa


Weekly - 1

Total - 59

Teaching language



Available soon


    1. Liljas,A., Liljas, L., Ash, M.-R.,Lindblom, G., Nissen, P., Kjeldgaard, M. Textbook of Structural Biology, 2nd ed., World Scientific, 2017
    2. Leach, A. R., Molecular Modelling: Principles and Applications, 2nd ed., Prentice Hall, 2001
    3. Hinchliffe, A., Molecular modelling for beginners, 2nd ed., Wiley, 2008
    4. Frenkel, D., Smit, B., Understanding molecular simulation. From algorithms to applications, 2nd ed., Academic Press, 2001
    5. Allen, M.P, Tildesley, D.J.,Computer simulation of liquids, 2nd ed., Oxford University Press, 2017
    6. Chemoinformatics: Basic Concepts and Methods, eds. Thomas Engel and Johann Gasteiger, Wiley-VCH, 2018.
    7. Leach, A. R.; Gillet, V. J. An Introduction to Chemoinformatics, 2ª ed.; Springer: Dordrecht, 2007.
    8. Applied Chemoinformatics: Achievements and Future Opportunities, eds. Thomas Engel and Johann Gasteiger, Wiley-VCH, 2018.
    9. Key papers from diverse fields.

Teaching method

Classes will consist in a mix of classical lectures and practical classes using computers and state of the art software on the different areas. The practical classes will be implemented with the students organised in small groups (2 or 3 students), developing protocols aimed at giving practical experience with the methodologies using real situations. There will be tutor/s helping the students developing these protocols.

Evaluation method

Evaluation consists on the evaluation of practical classes (50%) and final exam (50%). A minimum mark of 9.5 should be obtained in each individual component. The evaluation of practical classes will be done by analysing the written answers of the students in the protocols and/or presentations of papers/topics.

Subject matter

The topics in this curricular unit are very varied, reflecting the diverse methodologies present in the field. The topics below aim at covering the majority of the field with different depths of coverage.

  1. Introduction to structural biology, experimental techniques for structural determination and databases of structural data.

  2. Representation and visualisation of molecular structures.

  3. Statistical mechanics in biomolecular modelling.

  4. Molecular mechanics/dynamics.

  5. Molecular docking.

  6. Protein structure prediction.

  7. Quantitative Structure-Activity Relationships (QSAR).

  8. Introduction to drug discovery using structural bioinformatics methods.