Uploaded July 2026 | Updated September 2026, 2 weeks ago
There is sooooo much you can do with the PDB (way more than I even know how to do) and the details are too complex to try to explain here, but thankfully, the PDB is also an educational resource! “The PDB” is actually a multi-continent collaboration with several different centers. The one based out of the US is the the Research Collaboratory of Structural Bioinformatics (RCSB) PDB, and they have a great website called PDB-101: pdb101.rcsb.org
Some of the features you’ll want to be sure to check out:
- Structure Summary page: provides an overview of a structure - measurements of the quality of the structural model and underlying data, a description of what the structure contains, information about the source of the sample, information about the experimental method, and links to any accompanying paper and other related structures
- Validation Reports, including 3D view - points out potential problems with the structural model’s geometry (bond angles, etc.) and clashes (atoms too close in space) as well as places the model doesn’t match the data well. More here: thebumblingbiochemist.com/365-days-of-science/structurequality & youtu.be/0AswlZBLpKw
- 3D Sequence Viewer - maps annotations like functional sites to the 3D structure. More here: youtu.be/6zKBBkzl-4A
- Advanced Search Query Builder - allows you to search for proteins based on similar sequences, structures, motifs, experimental methods, ligands, etc., narrowing things down using logic operators (AND/OR/NOT) etc. to find exactly what you want. More here: youtu.be/iSM6orTve-Y
- Pairwise Structure Alignment - compare structures based on their shapes - Unlike Clustal, which aligns protein sequences based on their sequences, the PDB Pairwise Structure Alignment tool aligns one or more structures (experimentally-determined or predicted) and their sequences to a reference structure and sequence based on their shapes. More here: youtu.be/MOBMBuAIAKo
- RCSB Help Guide - super detailed guide to all things PDB, with hyperlinked examples, etc. rcsb.org/docs/tools/pairwise-structure-alignment
- PDB 101: Great educational and teaching resources, as well as a fun molecule of the month feature: If you go to this page in the “learn” tab, you’ll find this Introduction to PDB Data: pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/introduction
More on the PDB: bit.ly/thepdb & bit.ly/pdbstructures
PDB YouTube playlist: youtube.com/playlist?list=PLU1mvOopp1lk&si=LLBBOZkQfvOX-Yle
More on Uniprot: bit.ly/uniprotprotparam
More on other tools for working with proteins: thebumblingbiochemist.com/365-days-of-science/proteintools
Structural biology resources guide: bit.ly/structural_biology
My structural biology YouTube playlist: youtube.com/playlist?list=PLUWsCDtjESrGhwVxsRbTJdL-BEsN60RCs
My x-ray crystallography YouTube playlist: youtube.com/playlist?list=PLUWsCDtjESrHIGzgUctYRWSWm-lw9_VhX
more on crystallography here: bit.ly/xraycrystallography2
more about all sorts of things: #365DaysOfScience All (with topics listed) 👉 bit.ly/2OllAB0 or search blog: thebumblingbiochemist.com
⠀
#scicomm #biochemistry #molecularbiology #biology #sciencelife #science #realtimechem
There is sooooo much you can do with the PDB (way more than I even know how to do) and the details are too complex to try to explain here, but thankfully, the PDB is also an educational resource! “The PDB” is actually a multi-continent collaboration with several different centers. The one based out of the US is the the Research Collaboratory of Structural Bioinformatics (RCSB) PDB, and they have a great website called PDB-101: pdb101.rcsb.org
Some of the features you’ll want to be sure to check out:
- Structure Summary page: provides an overview of a structure - measurements of the quality of the structural model and underlying data, a description of what the structure contains, information about the source of the sample, information about the experimental method, and links to any accompanying paper and other related structures
- Validation Reports, including 3D view - points out potential problems with the structural model’s geometry (bond angles, etc.) and clashes (atoms too close in space) as well as places the model doesn’t match the data well. More here: thebumblingbiochemist.com/365-days-of-science/structurequality & youtu.be/0AswlZBLpKw
- 3D Sequence Viewer - maps annotations like functional sites to the 3D structure. More here: youtu.be/6zKBBkzl-4A
- Advanced Search Query Builder - allows you to search for proteins based on similar sequences, structures, motifs, experimental methods, ligands, etc., narrowing things down using logic operators (AND/OR/NOT) etc. to find exactly what you want. More here: youtu.be/iSM6orTve-Y
- Pairwise Structure Alignment - compare structures based on their shapes - Unlike Clustal, which aligns protein sequences based on their sequences, the PDB Pairwise Structure Alignment tool aligns one or more structures (experimentally-determined or predicted) and their sequences to a reference structure and sequence based on their shapes. More here: youtu.be/MOBMBuAIAKo
- RCSB Help Guide - super detailed guide to all things PDB, with hyperlinked examples, etc. rcsb.org/docs/tools/pairwise-structure-alignment
- PDB 101: Great educational and teaching resources, as well as a fun molecule of the month feature: If you go to this page in the “learn” tab, you’ll find this Introduction to PDB Data: pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/introduction
More on the PDB: bit.ly/thepdb & bit.ly/pdbstructures
PDB YouTube playlist: youtube.com/playlist?list=PLU1mvOopp1lk&si=LLBBOZkQfvOX-Yle
More on Uniprot: bit.ly/uniprotprotparam
More on other tools for working with proteins: thebumblingbiochemist.com/365-days-of-science/proteintools
Structural biology resources guide: bit.ly/structural_biology
My structural biology YouTube playlist: youtube.com/playlist?list=PLUWsCDtjESrGhwVxsRbTJdL-BEsN60RCs
My x-ray crystallography YouTube playlist: youtube.com/playlist?list=PLUWsCDtjESrHIGzgUctYRWSWm-lw9_VhX
more on crystallography here: bit.ly/xraycrystallography2
more about all sorts of things: #365DaysOfScience All (with topics listed) 👉 bit.ly/2OllAB0 or search blog: thebumblingbiochemist.com
⠀
#scicomm #biochemistry #molecularbiology #biology #sciencelife #science #realtimechem
