Sumários
Block 04 - Class 04: Evaluation
17 Dezembro 2021, 14:00 • Miguel Machuqueiro
The students presented their reports and benchmarks on pKa calculations of selected protein structures.
Block 04 - Class 04: Evaluation
17 Dezembro 2021, 09:30 • Miguel Machuqueiro
The students presented their reports and benchmarks on pKa calculations of selected protein structures.
Block 04 - Class 03: Introduction to molecular dynamics (MD)
10 Dezembro 2021, 14:00 • Miguel Machuqueiro
The basic concepts of MD simulations are introduced and the students should learn the workflow needed to perform MD simulations of a protein system: system setup, energy minimization, initialization of temperature and pressure, and finally, perform some common trajectory analyses. A more detailed interpretation of the results is provided, including some strategies on how to plot them with rigor and scientific quality.
Block 04 - Class 03: Introduction to molecular dynamics (MD)
10 Dezembro 2021, 09:30 • Miguel Machuqueiro
The basic concepts of MD simulations are introduced and the students should learn the workflow needed to perform MD simulations of a protein system: system setup, energy minimization, initialization of temperature and pressure, and finally, perform some common trajectory analyses. A more detailed interpretation of the results is provided, including some strategies on how to plot them with rigor and scientific quality.
Block 04 - Class 02: pH Effects in drugs and proteins and how to calculate pKa values from a protein 3D structure
3 Dezembro 2021, 14:00 • Miguel Machuqueiro
We presented the molecular details of how pH can influence protein stability and drug bioavailability. We also introduce a simple method to estimate the protein pKa values using a Poisson-Boltzmann-based predictor developed in-house (www.pypka.org).