Data Exploration Services
2018 RCSB.org Statistics
RCSB PDB's website at rcsb.org was visited each month by an average of 448,925 unique visitors and >1 million unique visits. More than 37 TB of data were accessed. Traffic is tracked using AWstats. RCSB.org is visited by >1 million unique visitors/year.
| Month | Unique Visitors | Visits | Bandwidth |
|---|---|---|---|
| January 2018 | 469,866 | 1,308,127 | 3123.22 GB |
| February 2018 | 434,550 | 1,208,166 | 2719.71 GB |
| March 2018 | 500,382 | 1,411,474 | 2578.50 GB |
| April 2018 | 495,318 | 1,436,498 | 1976.61 GB |
| May 2018 | 493,052 | 1,962,823 | 3264.53 GB |
| June 2018 | 455,755 | 1,471,167 | 2638.91 GB |
| July 2018 | 441,657 | 1,435,199 | 2182.62 GB |
| August 2018 | 426,638 | 1,336,378 | 1921.11 GB |
| September 2018 | 489,292 | 1,550,503 | 2473.55 GB |
| October 2018 | 567,457 | 1,845,545 | 3497.92 GB |
| November 2018 | 582,762 | 1,862,634 | 3865.92 GB |
| December 2018 | 532,347 | 1,769,555 | 2589.80 GB |
Time-stamped Copies of the PDB Archive
A snapshot of the PDB archive (ftp://ftp.wwpdb.org) as of January 1, 2018 has been added to ftp://snapshots.wwpdb.org and ftp://snapshots.pdbj.org. Snapshots have been archived annually since 2005 to provide readily identifiable data sets for research on the PDB archive.
The directory 20190101 includes the 147,610 experimentally-determined structure and experimental data available at that time. Atomic coordinate and related metadata are available in PDBx/mmCIF, PDB, and XML file formats. The date and time stamp of each file indicates the last time the file was modified. The snapshot is 1,529 GB.
Explore PDB Statistics
A variety of PDB statistics are available; including the distribution of structures released per year, and refinement software used. Visualization of PDB Data Distribution by Enzyme Classification allows users to interactively explore the enzyme classes in the PDB.
3D View Features
The 3D View at RCSB.org offers options for macromolecular-ligand interactions and X-ray electron density maps using NGL. Ligand interaction viewing options include hydrogen bonds, hydrophobic contacts, halogen bonds, pi interactions, and metal interactions. A 3D View User Guide is available.
Pi stacking and Cation-pi interaction of amitriptyline (ligand ID TP0) as seen in the A variant of human alfa1-acid glycoprotein (PDB structure 3APV).
NGL displays 2fo-fc (blue mesh/surface) and fo-fc (red/green mesh/surface) maps in the context of the structural model for X-ray crystallographic structures. Electron density maps combine the structural model (coordinates) and the experimentally-collected data from an X-ray structure determination and serve to represent the fit of the model to the data. Even in the best quality structures, there are areas of poor electron density, which may represent sections of the model that exist in multiple conformations. For more information, see the User Guide or learn more about Structure Factors and Electron Density at PDB-101.
Close up view of the electron density around the inhibitor (ligand ID R36) seen in complex with plasmepsin (PDB structure 1LEE; zoom in to get same view).
2018 Papers Published
Investigation of protein quaternary structure via stoichiometry and symmetry ınformation (2018) PLoS ONE 1: e0197176. doi: 10.1371/journal.pone.0197176
Recon3D enables a three-dimensional view of gene variation in human metabolism (2018) Nature Biotechnology 36: 272–281 doi: 10.1038/nbt.4072
Automated evaluation of quaternary structures from protein crystals (2018) PLoS Comput Biol 14: e1006104 doi: 10.1371/journal.pcbi.1006104
Analyzing the symmetrical arrangement of structural repeats in proteins with CE-Symm (2018) bioRxiv doi: 10.1101/297960
NGL viewer: web-based molecular graphics for large complexes (2018) Bioinformatics 34: 3755–3758. doi: 10.1093/bioinformatics/bty419