Chemistry

CHM 4413L: Biophysical Lab (Spring 2025)

In addition to what is on this guide, here are some additional tips for finding information about particular proteins and enzymes:

1) Search for primary literature

Check out the Search Tips and Finding Journal Articles tabs for more information.

I recommend trying your search in Web of Science and/or PubMed. Think about keywords and how broad/narrow you should be in your information gathering.

2) Find your protein in the RCSB Protein Data Bank

The RCSB Protein Data Bank (PDB) is the largest repository for experimental protein structure data, sourced by biologists and biochemists around the world.

Each deposited structure is assigned a PDB identifier (PDB ID). Unlike other molecular identifiers, which are uniquely assigned to specific molecules, a given biomolecule may have several structures in the PDB in different conformations or under different experimental conditions. Each structure has it's own PDB ID. 

Some tips:

• If the regular search bar does not autofill what you need, use the "Advance Search" options. Make sure your query is not entered in as a residue sequence!
• Use the refinement column to limit the structures you retrieve (like "organism - homo sapiens")

3) Find your protein in PubChem

PubChem is a free, public database maintained by the National Library of Medicine. It is a good place to find links out to other sources related to your specific protein. 

Some tips:

• Anytime you see "Evidence PMID" - use that link to find the primary literature source.
• Browse each section to see what kinds of information PubChem has put together.
• Look in the "Information Sources" section for links out to other datasets. For example, UniProt contains information about enzyme activity, kinetics, and pathways. 

4) Citation chain your protein in Web of Science

Web of Science has the best in class "citation chaining," which means that you can enter in one source and see who else has cited that source. Grab the DOI for the primary report of your protein structure in the PDB and look for it in Web of Science.

Some tips:

• Look for "Citations" on the right side - this link will bring together articles that cited the protein structure you found.
• Try using the "Refine results" column to narrow your results.

Citation chaining is useful for all kinds of searches because you can track a scientific idea through time. I recorded a video last year might be helpful if you want to learn more. Always feel free to reach out to me for more help!

Nolan: "Using One Source to Find More with Citation Chaining" on Vimeo