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index.qmd
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---
title: "StrBio UAM"
author:
name: Modesto
affiliation: Department of Biochemistry, School of Medicine, UAM
date: "August 21, 2023"
date-modified: "`r Sys.Date()`"
suppress-bibliography: true
toc: false
toc_float: false
format:
html:
page-layout: full
theme: simplex
toc: false
---
```{r}
```
# About
::: {style="float: right; position: relative; top: 0px; padding: 9px;"}
{fig-align="right"}
:::
This is a [Quarto](https://quarto.org/) site containing the materials for the *Structural Bioinformatics* course in the [Master's Degree in Bioinformatics & Computational Biology \@UAM](https://www-uam-es.translate.goog/Medicina/MasterBioinformaticaBiologiaComputacional/1446820907497.htm?language=es&nodepath=M?ster+Universitario+en+Bioinform?tica+y+Biolog?a+Computacional&_x_tr_sl=es&_x_tr_tl=en&_x_tr_hl=es&_x_tr_pto=wapp). All these materials are open access and shared under [CC BY-NC license](https://creativecommons.org/licenses/by-nc/2.0/ "CC BY-NC license"). These materials were originally elaborated for the 2022 course edition and is subsequently revised each year. The current Course syllabus for year 2024-2025 can be found [here](2024_33082_es.pdf) (in Spanish). Detailed academic information about the course contents, dates and assessment only can be found at the UAM [Moodle](https://posgrado.uam.es/) site.
::: callout-note
This is primarily an introductory course (3 ECTS), designed to offer a general overview as well as tools and resources necessary for initiating SB research projects. Consequently, many fundamental concepts in protein biophysics, scripting tools for SB, and deep-learning methods will only be briefly covered.
:::
In addition to some already classic books, reviews, and articles referenced, the content also draws heavily on the work of others who have generously shared their course materials, tips, and resources on their blogs or websites, as well as discussions on Twitter, especially during the Alphafold2 revolution in 2020-2021. Notable contributions from [Alexandre Bovin](https://www.uu.nl/staff/amjjbonvin), [Sergey Ovchinnikov](https://twitter.com/sokrypton), [Martin Steinegger](https://twitter.com/thesteinegger) and [Carlos Outeiral](https://twitter.com/c_outeiral?lang=es), among many others. Every effort has been made to acknowledge and link to these contributions; however, I apologize in advance for any that may have been inadvertently omitted.
The course includes three hands-on exercises designed to guide you through using Pymol to visualize molecules and model proteins via homology modeling and AlphaFold. [Additionally, several exercises and questions are highlighted in green throughout the sections to encourage you to reflect on the knowledge and skills acquired and to delve deeper into interpreting the results.]{style="color:green"}
I suggest you review also the Structural Bioinformatics exercises from Pontificia Universidad Católica de Chile, detailed in [Engelberger et al. (2021)](https://pubs.acs.org/doi/10.1021/acs.jchemed.1c00022): <https://github.com/pb3lab/ibm3202>
::: callout-warning
# Under construction
## ❗ Check the modification date.
Please be aware that this website is a draft and will be revised throughout the semester (Feb-May 2025). The English writing style is been enhanced with the assistance of Microsoft Copilot (UAM license).
Feedback, assistance, and suggestions are welcome.
:::
## 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](mailto::[email protected]), [{{< iconify fa6-brands x-twitter >}}(f.k.a. Twitter)](https://twitter.com/mredrejo "Twitter") or [{{< iconify simple-icons bluesky >}}](https://bsky.app/profile/mredrejo.bsky.social).