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Collects NMR data from any experiment and captures assigned chemical shifts, coupling constants, and peak lists for a variety of macromolecules; contains derived annotations such as hydrogen exchange rates, pKa values, and relaxation parameters.
Rich information about all PDB entries, multiple search and browse facilities, advanced services including PDBePISA, PDBeFold and PDBeMotif, advanced visualisation and validation of NMR and EM structures, tools for bioinformaticians.
Supports browsing in multiple languages such as Japanese, Chinese, and Korean; SeSAW identifies functionally or evolutionarily conserved motifs by locating and annotating sequence and structural similarities, tools for bioinformaticians, and more.
Simple and advanced searching for macromolecules and ligands, tabular reports, specialized visualization tools, sequence-structure comparisons, RCSB PDB Mobile, Molecule of the Month and other educational resources at PDB-101, and more.
The Office of Research Integrity (ORI) of the U.S. Department of Health and Human Services has announced their final Research Misconduct Finding in the case of H.M. Krishna Murthy. The Administrative Law Judge found that Murthy reported falsified and/or fabricated research in 10 journal publications and 12 corresponding PDB structures. Per wwPDB policies, all 12 PDB structures in question have been obsoleted. The Judge’s finding was the result of years of work on the part of the dedicated ORI legal team, who were assisted by members of the US regional data centre of the wwPDB and expert structural biologists. Mandatory PDB deposition of both atomic coordinates and experimental data were critical to resolving this case.
Depositors can help the structure modeling community test prediction methods by marking depositions as a CASP target in OneDep. A wide range of targets are needed, with particular interest in membrane proteins, protein complexes, and cryo-EM structures. CASP will also include modeling efforts assisted by sparse experimental data, in collaboration with experimental groups in NMR, SAXS, SANS, crosslinking, and FRET.
Validation reports for all PDB structures have been updated to include new percentile statistics reflecting the state of the archive on December 31st 2017 and updated versions of third-party software: CCP4/Refmac (7.0 v44), Phenix (1.13) and Mogul (2018) and CSD archive (as539be). The LLDF statistic previously used to identify ligands that do not fit electron density well has been replaced by a combination of Real-space R-factor (RSR>0.4) and Real-space correlation coefficient (RSCC<0.8). The identification of standard amino acid or nucleotide residues that do not fit the electron density well has been corrected to take into account how reliably Refmac software reproduces the R-factors reported by authors. Documentation at wwpdb.org/validation has been updated to reflect these changes.