The protein biochemist’s toolbox almost definitely includes UniProt & ProtParam. So here are some of the basics of using these and other free online database tools to learn more about proteins. With UniProt as a launchpad you can search for proteins of interest, get their sequences, align them, find similar ones, look at their domains & where else those domains occur, figure out their likely charged-ness (from pI), their extinction coefficient (for measuring concentration with UV light), and way more. You can do way way more but I’m going to focus on the basic things I use a lot and give you an overview of what the way way more things include. 

I’m not gonna write much today, just a show-and-tell, but here are links to the tools and links to past posts about some of the things I talked about. I’ll also put some graphics



Tools:

UniProt (this is your basic starting point for finding & learning about a protein – it connects you to way more resources through like a bazillion links & lets you align sequences): https://www.uniprot.org/ 

ExPasy ProtParam (this lets you calculate pI, molecular weight, extinction coefficient, & more): https://web.expasy.org/protparam/

Past posts: 

more about the PDB: https://bit.ly/pdbstructures    

more about using the extinction coefficient to find protein concentration based on UV absorbance: http://bit.ly/proteinmeasuring 

more about pI, protein charge, and ion exchange chromatography: http://bit.ly/ionexchangechromatography 

more about proteins & how they get their structure: https://bit.ly/proteinstructure 

more about PyMol: https://bit.ly/pymolintro & https://bit.ly/pymolmovies   

more about Ago: https://bit.ly/agostructurestuff  

more about x-ray crystallography: http://bit.ly/xraycrystallography2   

more about cryoEM: https://bit.ly/cryoEMbumblyintro  

more about Ago: https://bit.ly/agostructurestuff  

more about all sorts of things:  #365DaysOfScience All (with topics listed) 👉 http://bit.ly/2OllAB0 or search blog: https://thebumblingbiochemist.com     


Leave a Reply

Your email address will not be published.