Sumários

Block 04 - Class 03: Study the S100B/Antibody interactions using Molecular Dynamics

2 Dezembro 2022, 09:00 • Miguel Machuqueiro

The basic concepts of MD simulations are introduced and the students should learn the workflow needed to perform MD simulations of protein systems: system setup, energy minimization, initialization of temperature and pressure, and finally, perform some common trajectory analyses. We studied the case of the S100B:nanobody complex and performed a more detailed interpretation of the results, including some strategies on how to plot them with rigor and scientific quality.

Block 04 - Class 02: Molecular Docking of S100B protein with its single domain antibody using the HADDOCK webserver

25 Novembro 2022, 14:00 • Miguel Machuqueiro

We introduce the basic concepts of molecular docking and its applications to protein/protein docking. We used the structures from the S100B structure and the single domain structure (obtained from the previous class) in the HADDOCK server to sample different binding modes of the complex.

Block 04 - Class 02: Molecular Docking of S100B protein with its single domain antibody using the HADDOCK webserver

25 Novembro 2022, 09:00 • Miguel Machuqueiro

We introduce the basic concepts of molecular docking and its applications to protein/protein docking. We used the structures from the S100B structure and the single domain structure (obtained from the previous class) in the HADDOCK server to sample different binding modes of the complex.

Block 04 - Class 01: Tutorial on Molecular Visualization of the S100B Protein and 3D Structure Prediction of its Single Domain Antibody

18 Novembro 2022, 14:00 • Miguel Machuqueiro

In this class, we focused on molecular visualization skills using PyMOL, which will be important for the upcoming classes and used some online tools for protein structure prediction.

Block 04 - Class 01: Tutorial on Molecular Visualization of the S100B Protein and 3D Structure Prediction of its Single Domain Antibody

18 Novembro 2022, 09:00 • Miguel Machuqueiro

In this class, we focused on molecular visualization skills using PyMOL, which will be important for the upcoming classes and used some online tools for protein structure prediction.