StrBio 2023-24
About
This is a Quarto site containing the materials for the Structural Bioinformatics course of fall 2023 in the Master’s Degree in Bioinformatics & Computational Biology @UAM. All these materials is open access and it is shared under CC BY-NC license. Course syllabus is here (in Spanish). Detailed academic information about the course contents, dates and assessment only can be found at the UAM Moodle site.
In addition to some already classic books, reviews, and articles referenced, the content of this short course is also largely inspired by the work of others who have shared their course materials, tips, and other resources on their own blogs or websites and in discussions on Twitter, including Alexandre Bovin, Sergey Ovchinnikov, Martin Steinegger and Carlos Outeiral, among many others. I hace tried to acknowledge and link to each one of those contributions but I apologize in advance for those I may not have mentioned.
The course includes three hands-on exercises that will guide you through using Pymol to visualize molecules and modeling proteins through homology modeling and AlphaFold. In addition, there are several exercises/questions in some sections that are highlighted in green to motivate you to think about the knowledge and skills you have acquired and to go a little further in interpreting the results.
As a suggestion, I would also like to invite you to check the set of exercises on Structural Bioinformatics from the Pontificia Universidad Católica de Chile, described in Engelberger et al. (2021): https://github.com/pb3lab/ibm3202
Please note that this website is a draft that is still under development, and that the earliest I can expect to have a first complete version is by the end of the semester (December 2023). Any feedback, help, or suggestions would be greatly appreciated.
Contact
Please let me know if you find some mistake or a missing reference. Definitely, I’ll appreciate any suggestion, request or correction. You can reach me by email or