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UW-system software library
Protein Data Bank (PDB – 3D)
Worldwide PDB (wwPDB)
America’s PDB – Research Collaboratory for Structural Bioinformatics
Protein Data Bank in Europe
Protein Data Bank Japan
BMRB – Biological Magnetic Resonance Data Bank
PDB 101 / Molecule of the month
VIPERdb – Virus Particle Explorer.Scripps
3-Dimensional Electron Microscopy
Protein, DNA, RNA, genome sequence databases
Autodock / Autodock Vina Tutorials (HTML)
MODELLER Tutorials (HTML)
Practical Pymol for Beginners (HTML – 2018)
Introduction to PyMOL (PDF – 2009)
Sybyl Tutorials (HTML – 2002)
UCSF Chimera Tutorials (HTML)
UCSF ChimeraX Tutorials (HTML)
R / RSTudio tutorials
R for Beginners (E. Paradis – PDF)
R Tutorial (cyclist.org)
Learn R Programming (tutorialspoint.com)
Learn R Programming | R examples (datamentor.io)
R Course: R Tutorial for Beginners: Learning R Programming (guru99.com)
External tutorials: Software Carpentry
Databases and SQL
Cheat sheets can be useful as a memory back-up. When I learned Latin, it was stressed that before looking into the lexicon, one should first try to retrieve the information from memory first. It may be there. Then, if needed, look into cheat sheet, which can sometimes be a challenge too given the information concentration. Cheat sheets come in various formats, which can sometimes be called quick reference guide instead.
- PyMOL: PymolRef.pdf, PyMOL Cheat Sheet Source Code (zip)
- Chimera: quickref.pdf
- ChimeraX: User guide (HTML)
- VMD: vmd_cheatsheet.pdf, vmd-tutorial.pdf
RStudio / R
RStudio provides a large series of cheat sheets that encompass a wide range of subjects. The page is located at rstudio.com/resources/cheatsheets and covers R, python, R markdown and many specific R packages.