Structural biology resources – guide to my favorite software, articles, books, conferences and websites

Structural biology resources – guide to my favorite software, articles, books, conferences and websites

Homethe bumbling biochemistStructural biology resources – guide to my favorite software, articles, books, conferences and websites
Structural biology resources – guide to my favorite software, articles, books, conferences and websites
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Structural biology resources

downloadable version: https://docs.google.com/document/d/1H6EZLMWH29-9rmSJOwE0YoskdD75PBav/edit?usp=sharing&ouid=110501489579733284162&rtpof=true&sd=true

Educational resources

My stuff:
• If you need a refresher on x-ray crystallography, start here: http://bit.ly/xraycristallography2
• and I created a page on my blog that contains links to all my structural biology articles: https://bit.ly/structural_biology
• and here is a link to my structural biology YouTube playlist: https://youtube.com/playlist?list=PLUWsCDtjESrGhwVxsRbTJdL-BEsN60RCs
• here are some key articles:
o resolution: blog: https://bit.ly/structure_resolution; YouTube: https://youtu.be/Ijm-nDzLWhA https://youtu.be/1DZClUKowsY and this introductory video: YouTube: https://youtu.be/t5WeMkY0skU
• understand crystal structures: https://bit.ly/crystalstructuremodels & https://youtu.be/YK3VkqD2o2s
• introduction to PDB, crystal structure entries, crystal content, resolution: https://bit.ly/pdbstructures & https://youtu.be/Re2gwi-_OEw & https://youtu.be/IZtHsUFbye s

More official stuff:

If you're new to structural biology, start with PDB101!

The US-based PDB is the Research Collaboratory of Structural Bioinformatics (RCSB). PDB has an excellent website called PDB-101: http://pdb101.rcsb.org/
If you go to this page in the "learn" tab, you will find this introduction to PDB data: http://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/introduction as well as many pages on the basics of crystallography and crystal structures.

They also have lots of great resources for teachers and learners, including downloadable infographics and posters and DIY paper models. I used the GFP model when I taught a lesson at a summer camp: https://bit.ly/gfpfunscience Structural biology can be a little difficult to get into, so they have ways to draw you in, like their “Molecule of the Month” series. Each month they introduce a different molecule or class of molecules, tell you interesting things about them, and walk you through some structures.

X-ray crystallography

Books:
• Introduction to Macromolecular Crystallography, Second Edition, Alexander McPherson First published: March 11, 2008. Print ISBN: 9780470185902 | Online ISBN: 9780470391518 | DOI: 10.1002/9780470391518.
o I have had the pleasure of participating in the CSHL crystallography course twice and learning directly from Dr. McPherson (and a list of great crystallographers!). This book is really good and explains things in a complete but still understandable way! It doesn't get too much into the math and instead helps you get a more intuitive idea of what's going on. Highly recommend.
• Crystallography Made Crystal Clear: A Guide for Users of Macromolecular Models, Gale Rhodes. ISBN 0080455549, 9780080455549 https://books.google.com/books/about/Crystallography_Made_Crystal_Clear.html?id=rwnR6qvaWgkC&source=kp_book_description
o This is a more “meaty” book for those who really want to understand it.

Articles:
• “Protein crystallography for non-crystallographers, or how to get the most (but not more) from published macromolecular structures” by Alexander Wlodawer, Wladek Minor, Zbigniew Dauter and Mariusz Jaskolski. https://febs.onlinelibrary.wiley.com/doi/full/10.1111/j.1742-4658.2007.06178.x
o This is probably one of my most read articles. He does a great job explaining the basics of how to critically interpret the quality of protein crystal structures, what to watch for, and what basic statistics mean.
• Lamb, AL, Kappock, TJ and Silvaggi, NR (2015). You're Lost Without a Map: Navigating the Sea of Protein Structures. Biochimica et biophysica acta, 1854(4), 258-268. https://doi.org/10.1016/j.bbapap.2014.12.02

Websites:
• Resources for Crystallography Made Crystal Clear readers https://spdbv.vital-it.ch/TheMolecularLevel/CMCC/index.html
o It goes hand in hand with this book, but you don't need the book to enjoy it. It has links to TONS of useful software and articles for learning about crystallography.
• Protein crystallography course, Randy Read. Clear visuals and explanations. https://www-structmed.cimr.cam.ac.uk/course.html

Conferences:
• If you want to dive into the nitty-gritty of protein crystallography, Dr. Andrea Thorn has a great YouTube video series, “Macromolecular Crystallography Basics”: https://youtube.com/playlist?list=PLHHBmgJ8vFm6xZPlWlRGuBaoOM3OGlN5T .

Cryo-electron microscopy (cryo-EM)

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