Sumários
Módulo 4: Soft skills nas Ciências da Vida
18 Dezembro 2020, 09:30 • Cláudio Emanuel Moreira Gomes
Módulo 4: Soft skills nas Ciências da Vida. Carreiras - academia, industria e outras; artigos e publicações - o processo de publicação, seleção e ranking de revistas científicas. Bibliometria. Marketing em Ciência, os Cientistas nas redes sociais: visibilidade e impacto. Discussão prática.
Seminario de investigação
11 Dezembro 2020, 14:00 • Cláudio Emanuel Moreira Gomes
Seminario de investigação - Vibrational Spectroscopy for Chemical and Structural Characterization of Biomolecule pelo Prof. Francesco Simone Ruggeri, Department of Biomolecular Sciences, University of Wageningen
Class 03: Several analyses on the trajectory generated with MD simulations
4 Dezembro 2020, 09:30 • Miguel Machuqueiro
In this class, several analyses are performed to capture the stability of the simulations and the conformational transitions that were captured during the MD segment. These include RMSD, SAS, DSSP and the radius of gyration of the protein. A detailed interpretation of the results is provided, including some strategies on how to plot them with rigor and scientific quality.
Class 02: Setup a MD simulation system using GROMACS software package
27 Novembro 2020, 09:30 • Miguel Machuqueiro
In this class, we develop a system setup focused on the chosen protein using common bash scripts to call the GROMACS software package. Please note that in this tutorial the students will not be performing the simulations per se since these are very time-consuming. However, they can check out the input files and investigate the complete workflow: system building, energy minimization, initialization of temperature and pressure, and finally, they will perform some common trajectory analyses.
Class 01: Itroduction to Structure Visualization and Molecular Dynamics
20 Novembro 2020, 09:30 • Miguel Machuqueiro
In this class, we recap the fundamentals of molecular visualization skills using PyMOL, which will be important for the upcoming classes. The simpler skills you are expected to develop are viewing and manipulating molecular structures on the computer screen, and producing quality pictures for presentation or publication purposes. The basics of Molecular Dynamics are also presented. It is expected for students to get a feel of the workflow needed to perform molecular dynamics (MD) simulations. At the end, we also select a protein to be used in the MD workflow.