title: Molecular dynamics characterization of the conformational landscape of small peptides: A series of hands-on collaborative practical sessions for undergraduate students.
abstract: 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.
authors.affiliation: Computational Structural Biology Group, Bijvoet Center for Biomolecular Research, Faculty of Science-Chemistry, Utrecht University, Utrecht, The Netherlands.
authors.forename: João P G L M
authors.initials: JP
authors.lastname: Rodrigues
authors.affiliation: Biomedical Genomics, Hubrecht Insitute, KNAW & University Medical Center Utrecht, Utrecht, The Netherlands.
authors.forename: Adrien S J
authors.initials: AS
authors.lastname: Melquiond
authors.affiliation: Computational Structural Biology Group, Bijvoet Center for Biomolecular Research, Faculty of Science-Chemistry, Utrecht University, Utrecht, The Netherlands.
authors.forename: Alexandre M J J
authors.initials: AM
authors.lastname: Bonvin
mesh_terms: D003299:Cooperative Behavior; D006801:Humans; D007858:Learning; D056004:Molecular Dynamics Simulation; D010455:Peptides / Q000737:chemistry*; D011487:Protein Conformation; D013334:Students / Q000523:psychology; D013663:Teaching; D014495:Universities
chemical_list: D010455:Peptides
keywords: GROMACS; jigsaw teaching; molecular dynamics; protein modelling; virtualization