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abstracts
"The Structural Biology Knowledgebase (SBKB, http://sbkb.org) was established as a data aggregator to facilitate research design and analysis for a wide variety of biological systems. It serves as a single resource that integrates structure, sequence, and functional annotations plus technical information regarding protein production and structure determination. Researchers can search the SBKB by sequence, PDB ID or UniProt accession code, and receive an up-to-the-minute list of matching 3D experimental structures from the Protein Data Bank, pre-built theoretical models from the Protein Model Portal, annotations from 100+ open biological resources, structural genomics target histories and protocols from TargetTrack, and ready-to-use DNA clones from DNASU. It also possible to find structures according to functional relevance (KB-Rank tool), or find related technologies and publications from the PSI Technology and Publications Portals, respectively. Interactive tools such as real-time theoretical modeling and biophysical parameter prediction also enhance understanding of proteins that are not yet well characterized. Experimentally-focused ""hubs"" collect links to helpful tools and resources for the areas of Structural Targets; Structure, Sequence and Function; Homology Models, Methods and Technologies, and Membrane Proteins. In partnership with the Nature Publishing Group, latest research highlights and articles on specific biological systems are written monthly to share the impact of structural biology. This presentation will demonstrate how the SBKB turns data into knowledge and enables further research. SBKB is funded by a grant from the National Institute of General Medical Sciences of the National Institutes of Health (U01 GM093324)."
abstracts
In anticipation of continued growth in the number, size and complexity of the structures that are being studied and deposited in the PDB and EMDB, the Worldwide Protein Data Bank (wwPDB) has developed a new system for deposition and annotation of structural data. The new wwPDB Deposition & Annotation (D&A) system offers a single entry point for depositors from around the world to deposit X-ray, NMR, 3DEM data, receive detailed validation feedback, and preview annotations, all prior to submission. The system will assign not only PDB identifiers upon submission, but also EMDB and BMRB identifiers for 3DEM and NMR data, respectively. Furthermore, the new system is used at all wwPDB processing sites around the globe. After deposition, wwPDB annotators use the system for sequence annotation, ligand annotation, additional structure analysis and validation, and review. Validation functionality implements recommendations from the wwPDB X-ray Validation Task Force and produces a structure validation report for depositor review and submission to scientific journals. Depositors will have the option to use the new system or one of the legacy deposition tools (ADIT, AutoDep) through the end of 2014. At that time, the legacy tools will stop accepting new entries, and will only be available for a limited period of time to complete in-progress deposition sessions. An important feature of the new deposition system is its ability to accept and produce data in PDBx/mmCIF format, which has no limitations in the size or complexity of structures that can be represented. The PDBx/mmCIF Working Group, consisting of software developers from CCP4, Global Phasing Ltd., Phenix, and the wwPDB, have adapted structure determination software packages to produce PDBx/mmCIF format files suitable for deposition. The new wwPDB deposition and annotation will produce more consistent and higher quality archive entries, and will improve the efficiency and throughput of deposition and annotation. The modular design of the system will facilitate incorporating new functionalities and support for hybrid and other methods in the future. wwPDB members are RCSB PDB (supported by NSF, NIH, and DOE), PDBe (EMBL-EBI, Wellcome Trust, BBSRC, NIGMS, and EU), PDBj (NBDC-JST) and BMRB (NLM).
