Tutorial on Molecular Docking using the AutoDock suite

25 Outubro 2019, 14:00 • Miguel Machuqueiro

The process of drug discovery takes years to decades until a new drug is found, while also being very costly. Efforts to cut down the research timeline and costs by reducing lab experiments led to the use of computational modeling and, in particular, molecular docking calculations. In this tutorial, we will use the Autodock software to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. AutoDock has been widely-used and there are many examples of its successful application in the literature, including its application to AChE inhibitors, used here. We will test a strong AChE inhibitor (donepezil) and a milder compound (rosmarinic acid).

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Tutorial on Molecular Dynamics using GROMACS software package

18 Outubro 2019, 14:00 • Miguel Machuqueiro

With this tutorial, it is expected for students to get a feel of the workflow needed to perform molecular dynamics (MD) simulations with 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, like RMSD, SAS and the radius of gyration of the protein.

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Tutorial on Molecular Dynamics using GROMACS software package

18 Outubro 2019, 14:00 • Miguel Machuqueiro

With this tutorial, it is expected for students to get a feel of the workflow needed to perform molecular dynamics (MD) simulations with 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, like RMSD, SAS and the radius of gyration of the protein.

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Tutorial on molecular visualization using the software PyMOL

11 Outubro 2019, 14:00 • Miguel Machuqueiro

This tutorial intends to teach you some very simple techniques of molecular visualization, skills that can be useful to most people working in a (bio)chemical area. 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. This tutorial will be essential for the two next classes since Pymol will be used throughout the course.

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Tutorial on molecular visualization using the software PyMOL

11 Outubro 2019, 14:00 • Miguel Machuqueiro

This tutorial intends to teach you some very simple techniques of molecular visualization, skills that can be useful to most people working in a (bio)chemical area. 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. This tutorial will be essential for the two next classes since Pymol will be used throughout the course.

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