Sumários
Tutorial/Support for the project presentation
28 Novembro 2025, 09:00 • Bárbara Joana de Almeida Henriques
A tutorial class with the presence of all teachers to support the project presentation
Class 03: Study the S100B/Antibody interactions using Molecular Dynamics
21 Novembro 2025, 14:00 • Miguel Machuqueiro
The basic concepts of MD simulations were introduced, and students learned the workflow for performing MD simulations of protein systems: system setup, energy minimization, initialization of temperature and pressure, and finally, performing common trajectory analyses. We studied the S100B:nanobody complex and provided a more detailed interpretation of the results, including strategies for rigorously and scientifically plotting them.
Class 03: Study the S100B/Antibody interactions using Molecular Dynamics
21 Novembro 2025, 09:00 • Miguel Machuqueiro
The basic concepts of MD simulations were introduced, and students learned the workflow for performing MD simulations of protein systems: system setup, energy minimization, initialization of temperature and pressure, and finally, performing common trajectory analyses. We studied the S100B:nanobody complex and provided a more detailed interpretation of the results, including strategies for rigorously and scientifically plotting them.
Class 02: 3D Structure Prediction of Single Domain Antibody selective for S100B and Molecular Docking calculations of their interaction
14 Novembro 2025, 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 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
14 Novembro 2025, 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 S100B structure and the AI-generated single-domain structure in the HADDOCK server to sample different binding modes of the complex.