Sumários
Class 03: Study the S100B/Antibody interactions using Molecular Dynamics
6 Dezembro 2024, 09:00 • Miguel Machuqueiro
The basic concepts of MD simulations are introduced and the students learned 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.
Class 02: 3D Structure Prediction of Single Domain Antibody selective for S100B and Molecular Docking calculations of their interaction
29 Novembro 2024, 14:00 • Miguel Machuqueiro
We introduced the AI-assisted structural prediction tools using both the ESM Atlas and AlphaFold 3 servers. The basic concepts of molecular docking and its applications to protein/protein docking were also addressed. We used the structures from the S100B structure and the AI-generated single domain structure in the HADDOCK server to sample different binding modes of the complex.
Class 02: 3D Structure Prediction of Single Domain Antibody selective for S100B and Molecular Docking calculations of their interaction
29 Novembro 2024, 09:00 • Miguel Machuqueiro
We introduced the AI-assisted structural prediction tools using both the ESM Atlas and AlphaFold 3 servers. The basic concepts of molecular docking and its applications to protein/protein docking were also addressed. We used the structures from the S100B structure and the AI-generated single domain structure in the HADDOCK server to sample different binding modes of the complex.
Class 01: Molecular Visualization of the S100B Protein
22 Novembro 2024, 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. We introduce the basic concepts of structural alignment and protein structure comparison. We also performed an advanced hydrophobicity analysis on the same protein.
Class 01: Molecular Visualization of the S100B Protein
22 Novembro 2024, 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. We introduce the basic concepts of structural alignment and protein structure comparison. We also performed an advanced hydrophobicity analysis on the same protein.