Molecular dynamics simulations and analysis for bioinformatics undergraduate students

Gonçalo C. Justino; Catarina P. Nascimento; Marta C. Justino

doi:10.1002/bmb.21512

journal article Apr 12, 2021

Molecular dynamics simulations and analysis for bioinformatics undergraduate students

Gonçalo C. Justino

Catarina P. Nascimento Marta C. Justino

Biochemistry and Molecular Biology Education Vol. 49 No. 4 pp. 570-582 · Wiley

View at Publisher Save 10.1002/bmb.21512

Abstract

AbstractA computational biochemistry laboratory, fitted for bioinformatics students, is presented. The molecular dynamics package GROMACS is used to prepare and simulate a solvated protein. Students analyze the trajectory with different available tools (GROMACS and VMD) to probe the structural stability of the protein during the simulation. Students are also required to make use of Python libraries and write their own code to probe non‐covalent interactions between the amino acid side chains. Based on these results, students characterize the system in a qualitatively approach but also assess the importance of each specific interaction through time. This work mobilizes biochemical concepts and programming skills, fostering critical thinking and group work and developing presenting skills.

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Details

Published: Apr 12, 2021
Vol/Issue: 49(4)
Pages: 570-582
License: View

Authors

G

Gonçalo C. Justino

Centro de Química Estrutural Instituto Superior Técnico, Universidade de Lisboa Lisbon Portugal; Escola Superior de Tecnologia do Barreiro Instituto Politécnico de Setúbal Lavradio Portugal

C

Catarina P. Nascimento

Escola Superior de Tecnologia do Barreiro Instituto Politécnico de Setúbal Lavradio Portugal

M

Marta C. Justino

Escola Superior de Tecnologia do Barreiro Instituto Politécnico de Setúbal Lavradio Portugal; Centro Interdisciplinar de Ciências Químicas e Biológicas Instituto Politécnico de Setúbal Lavradio Portugal

Cite This Article

Gonçalo C. Justino, Catarina P. Nascimento, Marta C. Justino (2021). Molecular dynamics simulations and analysis for bioinformatics undergraduate students. Biochemistry and Molecular Biology Education, 49(4), 570-582. https://doi.org/10.1002/bmb.21512

Molecular dynamics simulations and analysis for bioinformatics undergraduate students

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