Educational Outreach and User Training at the Worldwide Protein Data Bank

The Protein Data Bank (PDB) contains a wealth of structural and functional knowledge about proteins, RNA, DNA, and other macromolecules, and their assemblies and complexes with small molecules. The challenge faced by the providers of PDB data is to make this knowledge accessible to an increasingly large and diverse audience, ranging from expert structural biologists to non-specialist consumers of structural information. Educators, students, and general audiences will have their own specific interests and expectations from molecular structure data. For a general user, a 2D image of hemoglobin illustrates how a protein looks at a microscopic level. For high school students and educators, 3D models or computer graphics can show how one or a few specific proteins can assemble into an icosahedral virus. In contrast, PhD and post-doc level researchers require expert guidance on how to critically assess the quality of structural data, and in-depth training on the use of specialist tools and resources for the comparison and analysis of structures. The PDB archive is managed by members of the Worldwide Protein Data Bank (wwPDB): the Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB; rcsb.org), Protein Data Bank in Europe (PDBe; pdbe.org), Protein Data Bank Japan (PDBj), and BioMagResBank (BMRB, bmrb.wisc.edu). In addition to managing and distributing structural data, the wwPDB partners are engaged in numerous outreach initiatives and user training programs. These efforts are vital to ensuring that these uniquely valuable data can be effectively accessed and used by research scientists, students, and educators alike. This talk will describe on-going wwPDB outreach efforts and highlight exciting new initiatives at the RCSB PDB, PDBe and PDBj.

New wwPDB validation pipelines for X-ray, NMR and 3DEM structures

The Protein Data Bank (PDB) is the single global archive of 3D biomacromolecular structure data. The archive is managed by the Worldwide Protein Data Bank (wwPDB; wwpdb.org) organisation through its partners, the Research Collaboratory for Structural Bioinformatics (RCSB PDB), the Protein Data Bank Japan (PDBj), the Protein Data Bank in Europe and the Biological Magnetic Resonance Bank (BMRB). Analogously, the Electron Microscopy Data Bank (EMDB) is managed by the EMDataBank (emdatabank.org) organisation. A few years ago, realising the needs and opportunities to assess the quality of biomacromolecular structures deposited in the PDB, the wwPDB and EMDataBank partners established Validation Task Forces (VTFs) to advice them on up-to-date and community-agreed methods and standards to validate X-ray, NMR and 3DEM structures and data. All three VTFs have now published their recommendations (1, 2, 3) and these are getting implemented as validation-software pipelines . The pipelines are integrated in the new joint wwPDB deposition and annotation system (http://deposit.wwpdb.org/deposition/). In addition, stand-alone servers are provided to allow practising structural biologists to validate models prior to publication and deposition (http://wwpdb.org/validation-servers.html). The validation pipelines and the output they produce (human-readable PDF reports and machine-readable XML files) will be described.