Alexandre Bonvin bio photo

Computational Structural Biology group focusing on dissecting, understanding and predicting biomolecular interactions at the molecular level.

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An article describing our experience in teaching molecular modelling to our chemistry bachelor students at Utrecht University has just appeared in Biochemistry and Molecular Biology Education (BAMBE), a Wiley journal:

It is the result of a computer practical that we put online and has been noticed by the editors of the special issue of BAMBE focused on the development of instructional materials for the molecular modeling of biochemical molecules.

Quoting the abstract of the paper:

“Molecular modelling and simulations are nowadays an integral part of research in areas ranging from physics to chemistry to structural biology, as well as pharmaceutical drug design. This popularity is due to the development of high-performance hardware and of accurate and efficient molecular mechanics algorithms by the scientific community. These improvements are also benefitting scientific education. Molecular simulations, their underlying theory, and their applications are particularly difficult to grasp for undergraduate students. Having hands-on experience with the methods contributes to a better understanding and solidification of the concepts taught during the lectures. To this end, we have created a computer practical class, which has been running for the past five years, composed of several sessions where students characterize the conformational landscape of small peptides using molecular dynamics simulations in order to gain insights on their binding to protein receptors. In this report, we detail the ingredients and recipe necessary to establish and carry out this practical, as well as some of the questions posed to the students and their expected results. Further, we cite some examples of the students’ written reports, provide statistics, and share their feedbacks on the structure and execution of the sessions. These sessions were implemented alongside a theoretical molecular modelling course but have also been used successfully as a standalone tutorial during specialized workshops. The availability of the material on our web page also facilitates this integration and dissemination and lends strength to the thesis of open-source science and education.”

This particular course has now been replaced by a new bachelor course in which modelling will be addressed, but with no time for a thorough modelling practical. Instead we developed a new master course for our Molecular and Cellular Life Sciences master on “Structural Bioinformatics and Modelling”.

This new modelling practical is freely available online from our website at: