Data Exploration Services

2019 RCSB.org Statistics

RCSB PDB's website at rcsb.org was visited in 2019 by millions of unique visitors. More than 96,000 TB of data were accessed. Traffic is tracked using AWstats.
 
Month Unique Visitors Visits Bandwidth
January 2019 550,630 1,755,684 3441.88 GB
February 2019 567,111 1,749,232 7049.39 GB
March 2019 616,125 1,902,174 8767.70 GB
April 2019 762,930 2,695,239 10549.01 GB
May 2019 685,154 2,296,252 8803.14 GB
June 2019 509,592 1,594,699 7380.16 GB
July 2019 475,721 1,352,191 7919.04 GB
August 2019 727,132 2,214,257 5726.36 GB
September 2019 805,340 2,162,593 8199.12 GB
October 2019 1,003,833 2,554,096 8363.06 GB
November 2019 993,025 3,348,232 12079.64 GB
December 2019 871,969 2,858,873 7873.71 GB

Introducing Mol*

Mol* is a new 3D molecular viewer that enables fast visualization of molecular structures and their corresponding data, along with high-quality rendering within the browser window.

The speed of Mol*, enabling visualization of huge structures in the browser and even on mobile devices, is achieved thanks to the use of binary CIF files, available as static files or delivered from the ModelServer and VolumeServer. This compressed format, delivering only the data that is required, ensures incredibly fast loading of both model and map data from PDB and EMDB entries. In addition to its speed, Mol* has a powerful rendering engine, enabling high quality visualization of molecular structures in various representations.

Mol* is a collaborative project between RCSB PDB, PDBe, and CETIEC.

View for Faustovirus (PDB 5j7v) at RCSB.org. Toggle between 3D viewers at the bottom of the display.


wwPDB News: Time-stamped Copies of PDB and EMDB Archives

A snapshot of the PDB Core archive (ftp://ftp.wwpdb.org) as of January 1, 2020 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 Snapshots have been archived annually since 2005 to provide readily identifiable data sets for research on the PDB archive.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 20200101 includes the 159,140 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 of PDB Core archive is 575 GB.

A snapshot of the EMDB Core archive (ftp://ftp.ebi.ac.uk/pub/databases/emdb/) as of January 1, 2020 can be found in ftp://ftp.ebi.ac.uk/pub/databases/emdb_vault/20200101/ and ftp://snapshots.pdbj.org/20200101/. The snapshot of EMDB Core archive contains map files and their metadata within XML files for both released and obsoleted entries (10370 and 130, respectively) and is 1.7 TB in size.

wwPDB News: Improved resolution of DOIs for PDB entries

PDB structure DOIs now return new wwPDB landing web-pages for each released PDB entry. These pages present basic information about the corresponding PDB structure, offer the model coordinate, experimental data and validation file downloads, and links to all the wwPDB partner websites. For an example, see https://doi.org/10.2210/pdb6qw9/pdb. 

wwPDB encourages scientific journals to link to these DOIs from articles that describe or utilize PDB data. Metadata associated with each PDB DOI have been updated to enable data mining  direct from the API offered by CrossRef.

The community should note that a new style of PDB identifiers are being gradually introduced in preparation for when the supply of the familiar four character codes will be exhausted. The new accession code format starts with a prefix "PDB_" and contains eight alphanumeric characters, with the last four characters identical to the legacy four-character codes.

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Senior Scientific Web Application Developer
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The RCSB PDB web development team creates state-of-the-art web applications using data exploration tools and 3D molecular visualizations.

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2019 Publications

  • RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy
    (2019) Nucleic Acids Research 47: D464–D474. doi:10.1093/nar/gky1004
  • BioJava 5: A community driven open-source bioinformatics library
     (2019) PLoS Comput Biol 15: e1006791. doi:10.1371/journal.pcbi.1006791
  • Analyzing the symmetrical arrangement of structural repeats in proteins with CE-Symm  (2019) PLoS Comput Biol 15: e1006842 doi:10.1371/journal.pcbi.1006842
  • Continuous Evaluation of Ligand Protein Predictions: A Weekly Community Challenge for Drug Docking (2019) Structure 27: 326-1335 doi:10.1016/j.str.2019.05.012
  • Molecular Graphics: Bridging Structural Biologists and Computer Scientists
     (2019) Structure 75: 451-454 doi:10.1016/j.str.2019.09.001
  • Bringing Molecular Dynamics Simulation Data into View
     (2019) Trends Biochem Sci 44: 902-913 doi:10.1016/j.tibs.2019.06.004
  • Assessment of protein assembly prediction in CASP13
     (2019) Proteins 87: 1190-1199 doi10.1002/prot.25795
  • Small angle X‐ray scattering‐assisted protein structure prediction in CASP13 and emergence of solution structure differences
    (2019) Proteins 87: 1298-1314 doi 10.1002/prot.25827