If you generate computationally predicted structure models, then you should know about ModelCIF! This extension of PDBx/mmCIF is designed specifically for these structures and aligns with PDB data representation.
Read more:
https://www.wwpdb.org/news/news?year=2023wwPDB: 2023 News
wwPDB: Worldwide Protein Data Bank
There are 337 new entries in the PDB this week, including this collection of structures from Lu et al. of DNA tensegrity triangles under different conditions - this 3D structure is known to self-assemble into macroscopic crystals. View all new entries at
http://pdbe.org/latestSearch the PDB archive ‹ PDBe ‹ EMBL-EBI
PDBe / PDB Search
The updated Chemical Component Dictionary (CCD) files at PDBe provide enriched chemical data including database mappings, physicochemical properties and standardised coordinates.
Find out more at
https://www.ebi.ac.uk/pdbe/news/enriched-chemical-component-files-pdbeEnriched chemical component files at PDBe | Protein Data Bank in Europe
There are 308 new entries in the PDB this week, including this collection of structures of the sheath-tube (8hdw), portal adaptor (8hds) and baseplate (7yfz) of a cyanophage, termed Pam3, isolated from Lake Chaohu in China. View all new entries at
http://pdbe.org/latestSearch the PDB archive ‹ PDBe ‹ EMBL-EBI
PDBe / PDB Search
Looking more closely at the average size of structures since 2014, we can see this recent increase more clearly. This is likely driven by the increase in EM structures, which favours structure determination of larger complexes. 9/10
That brings us to end of our run-through of how PDB data has changed through the years - how might it change again in the next 100,000 entries?
📃All graphs generated using data from PDBe search API. Find the notebook & run this yourself at https://github.com/PDBeurope/pdbe-api-training/blob/master/PDB_release_stats.ipynb 10/10
pdbe-api-training/PDB_release_stats.ipynb at master · PDBeurope/pdbe-api-training
Interactive Python notebooks for PDBe API training - pdbe-api-training/PDB_release_stats.ipynb at master · PDBeurope/pdbe-api-training
Looking at the average size of structures (by annotated assembly) in the PDB over time, we can see modest increases through the 1990s and 2000s, with a steeper increase in more recent years. 8/10
For EM structures since 2014, the trend is definitely towards higher resolution, with 3.5 - 4 Angstrom structures initially taking off, followed by 3 - 3.5 in 2016, 2.5 - 3 in 2018 and mor recently, a clear increase in 2 - 2.5 Angstrom structures. 7/10
Looking more closely at releases since 2014 and the 100k milestone for the PDB, we can see that the number of X-ray diffraction releases stays quite consistent at 10k structures per year, with all the recent growth coming from increases in EM structures. 5/10
For X-ray diffraction structures, we see that the number of releases at each resolution bin rises pretty consistently over time. There is in fact a slight trend towards more share of lower resolution structures in recent years. 6/10
