Uploaded July 2026 | Updated September 2026, 2 weeks ago
With over a quarter million structures, how do you actually find what you’re looking for in the PDB? Depends! Sometimes, you go straight to an entry you’re looking for using the 4/12 digit accession number (such as you find at the bottom of a paper). Other times, you get sent there from UniProt. And other times, you use the Advanced Search Query Builder in the PDB. That allows you to search based on similar sequences, structures, motifs, experimental methods, ligands, etc.
You can search for structures already in the database or ones that you upload. You can also search for specific motifs and search by tons of other things like specific ligands and/or experimental details, narrowing things down using logic operators (AND/OR/NOT) etc. to find exactly what you want. rcsb.org/search/advanced
The best way to learn is to try for yourself
But if you want a tour through some of the options….
Also, here are some additional tools to check out
Software tools and databases for working with proteins
Blog: thebumblingbiochemist.com/365-days-of-science/proteintools
PDF: drive.google.com/file/d/1G7OVk6G_AiYPJugIw_DHX-JxtIvLhOBB/view?usp=drive_link
YouTube: youtu.be/encoJwuD6Pk
* UniProt - basics (functions, length, sequence(s), isoforms, structures, interactions, etc. - lots of links to more detailed databases for each) uniprot.org/
* more about it on my blog: bit.ly/uniprotprotparam & YouTube: youtu.be/6oBsTykEeGI
* PDB (Protein DataBank) - protein structures rcsb.org (US-maintained site), ebi.ac.uk/pdbe (European-mantained site)
* more about it on my blog: bit.ly/pdbstructures & YouTube: youtu.be/Re2gwi-_OEw & youtu.be/IZtHsUFbyes
* AlphaFold Protein Structure Database (AFDB) - contains pre-computed predicted structures of single chains of proteins alphafold.ebi.ac.uk/
* AlphaFold - Predicts the structure of proteins, nucleic acids, and complexes. The server has more limited options than the stand-alone (GitHub) and ColabFold (Python notebook-based) versions, but uses the latest version of AlphaFold alphafoldserver.com/
* More on my blog: thebumblingbiochemist.com/365-days-of-science/interpreting-alphafold-predictions/
* Viewing protein structures (molecular visualization software) - there are 2 main tools, ChimeraX & PyMol, as well as other, web-based, tools such as Mol* and iCN3D. ChimeraX is fully free for academic use. PyMol has a free version with slightly limited functionality and academic labs often have a license for the full thing.
* ChimeraX home page: https://www.rbvi.ucsf.edu/chimerax/ & tutorials: https://www.rbvi.ucsf.edu/chimerax/tutorials.html
* PyMol: pymol.org/
* More about it on my blog bit.ly/pymolintro & YouTube: youtube.com/playlist?list=PLUWsCDtjESrG-46VDvPZfYPQyyXhZbGCN
* Expasy ProtParam - protein stats (amino acid composition (e.g. # of each amino acid, isoelectric point (pI) (for predicting overall charge at different pHs), extinction coefficient (for getting concentration from UV), etc.) can also use for custom sequences you copy and paste - great for recombinant expression constructs web.expasy.org/protparam/
* more about it on my blog: bit.ly/uniprotprotparam & YouTube: youtu.be/6oBsTykEeGI
* PDBSum - Easy way to automatically generate protein topology & domain diagrams & investigate interfaces ebi.ac.uk/thornton-srv/databases/pdbsum/
* Just upload or fetch a PDB file and it'll generate a bunch of things including: domain architecture diagram, secondary structure diagrams, topology map, diagram of and information about ligand-protein and protein-protein interactions (distances, types, etc.), information about pockets, tunnels, and channels
* HawkDock - Models protein-protein interactions and analyzes strength of interactions at a residue level basis (for either predicted structures or already-prepared PDB files) https://cadd.zju.edu.cn/hawkdock/
* 3D bio notes - you put in the PDB code for a structure, then this site integrates a ton of information about the protein from various sources and lets you see sites of mutations, etc. in 3D. Also good for a quick overview or on the go look when you don’t want to open PyMol. 3dbionotes.cnb.csic.es/ws
* H++ - Free web-based tool that takes a pdb file of a protein and predicts the protonation state of each amino acid residue at a pH of your choosing http://newbiophysics.cs.vt.edu/H++/index.php
* more about it on my blog: bit.ly/hplusplus
* ExplorEnz - official IUBMB info about enzymes and their classification enzyme-database.org/
* More about it on my blog: bit.ly/ec_numbers & YouTube: youtu.be/8yO1XEzoVIE
Finished in comments
With over a quarter million structures, how do you actually find what you’re looking for in the PDB? Depends! Sometimes, you go straight to an entry you’re looking for using the 4/12 digit accession number (such as you find at the bottom of a paper). Other times, you get sent there from UniProt. And other times, you use the Advanced Search Query Builder in the PDB. That allows you to search based on similar sequences, structures, motifs, experimental methods, ligands, etc.
You can search for structures already in the database or ones that you upload. You can also search for specific motifs and search by tons of other things like specific ligands and/or experimental details, narrowing things down using logic operators (AND/OR/NOT) etc. to find exactly what you want. rcsb.org/search/advanced
The best way to learn is to try for yourself
But if you want a tour through some of the options….
Also, here are some additional tools to check out
Software tools and databases for working with proteins
Blog: thebumblingbiochemist.com/365-days-of-science/proteintools
PDF: drive.google.com/file/d/1G7OVk6G_AiYPJugIw_DHX-JxtIvLhOBB/view?usp=drive_link
YouTube: youtu.be/encoJwuD6Pk
* UniProt - basics (functions, length, sequence(s), isoforms, structures, interactions, etc. - lots of links to more detailed databases for each) uniprot.org/
* more about it on my blog: bit.ly/uniprotprotparam & YouTube: youtu.be/6oBsTykEeGI
* PDB (Protein DataBank) - protein structures rcsb.org (US-maintained site), ebi.ac.uk/pdbe (European-mantained site)
* more about it on my blog: bit.ly/pdbstructures & YouTube: youtu.be/Re2gwi-_OEw & youtu.be/IZtHsUFbyes
* AlphaFold Protein Structure Database (AFDB) - contains pre-computed predicted structures of single chains of proteins alphafold.ebi.ac.uk/
* AlphaFold - Predicts the structure of proteins, nucleic acids, and complexes. The server has more limited options than the stand-alone (GitHub) and ColabFold (Python notebook-based) versions, but uses the latest version of AlphaFold alphafoldserver.com/
* More on my blog: thebumblingbiochemist.com/365-days-of-science/interpreting-alphafold-predictions/
* Viewing protein structures (molecular visualization software) - there are 2 main tools, ChimeraX & PyMol, as well as other, web-based, tools such as Mol* and iCN3D. ChimeraX is fully free for academic use. PyMol has a free version with slightly limited functionality and academic labs often have a license for the full thing.
* ChimeraX home page: https://www.rbvi.ucsf.edu/chimerax/ & tutorials: https://www.rbvi.ucsf.edu/chimerax/tutorials.html
* PyMol: pymol.org/
* More about it on my blog bit.ly/pymolintro & YouTube: youtube.com/playlist?list=PLUWsCDtjESrG-46VDvPZfYPQyyXhZbGCN
* Expasy ProtParam - protein stats (amino acid composition (e.g. # of each amino acid, isoelectric point (pI) (for predicting overall charge at different pHs), extinction coefficient (for getting concentration from UV), etc.) can also use for custom sequences you copy and paste - great for recombinant expression constructs web.expasy.org/protparam/
* more about it on my blog: bit.ly/uniprotprotparam & YouTube: youtu.be/6oBsTykEeGI
* PDBSum - Easy way to automatically generate protein topology & domain diagrams & investigate interfaces ebi.ac.uk/thornton-srv/databases/pdbsum/
* Just upload or fetch a PDB file and it'll generate a bunch of things including: domain architecture diagram, secondary structure diagrams, topology map, diagram of and information about ligand-protein and protein-protein interactions (distances, types, etc.), information about pockets, tunnels, and channels
* HawkDock - Models protein-protein interactions and analyzes strength of interactions at a residue level basis (for either predicted structures or already-prepared PDB files) https://cadd.zju.edu.cn/hawkdock/
* 3D bio notes - you put in the PDB code for a structure, then this site integrates a ton of information about the protein from various sources and lets you see sites of mutations, etc. in 3D. Also good for a quick overview or on the go look when you don’t want to open PyMol. 3dbionotes.cnb.csic.es/ws
* H++ - Free web-based tool that takes a pdb file of a protein and predicts the protonation state of each amino acid residue at a pH of your choosing http://newbiophysics.cs.vt.edu/H++/index.php
* more about it on my blog: bit.ly/hplusplus
* ExplorEnz - official IUBMB info about enzymes and their classification enzyme-database.org/
* More about it on my blog: bit.ly/ec_numbers & YouTube: youtu.be/8yO1XEzoVIE
Finished in comments
