CRESTANO - Common REst api for Structural ANnotation

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The Protein Data Bank in Europe (PDBe; pdbe.org) is one of the core resources at the European Bioinformatics Institute (EMBL-EBI). PDBe is a founding member of the Worldwide Protein Data Bank (wwPDB), which manages the PDB, the single global archive of biomacromolecular structure data. The other wwPDB partners are RCSB, PDBj and BMRB. PDBe has operated a deposition and annotation facility for PDB data since 1998. Over the years, PDBe has developed advanced tools and services for analysis of biomacromolecules (including unique tools such as PDBeFold, PDBePISA and PDBeMotif) and for delivery of PDB data to the user community. In addition, PDBe develops and maintains critical resources such as SIFTS (Structure Integration with Function, Taxonomy and Sequences), a vital source of up-to-date cross-reference information to other biological data resources.The Cambridge Crystallographic Data Centre (CCDC; www.ccdc.cam.ac.uk) manages the Cambridge Structural Database (CSD), the main archive for small-molecule crystal structure data. CSD contains structural data for organic and organometallic compounds obtained using single crystal X-ray and neutron diffraction methods or based on powder diffraction data. The archive was established in 1965 and now contains more than 600,000 structures of small molecules. In addition to archiving the small molecule structural data, CCDC has developed many tools for the analysis of these data.The information available in the PDB archive is used by structural biologists and the wider biomedical community to understand the structures archived in the PDB, while CSD data amongst many other applications can be used by chemists and biochemists for automatic screening of natural molecules suitable as drug candidates. Recently, to improve the annotation and validation of small molecule information in the PDB, wwPDB has entered into a collaboration with CCDC. As part of this, CCDC has made a number of tools available to the wwPDB partners, including Mogul, which will be used for validation of small molecule geometry during deposition and annotation of PDB data. This will constitute a major improvement as analysis of ligand structures in the PDB has shown that the majority of ligand models can be improved. The structure validation pipeline, which includes Mogul and which will become a critical part of the new wwPDB Deposition and Annotation system (D&A), is being developed at PDBe.The goal of the present project is to implement a web-services API that will provide access to biomacromolecular structure data and advanced analyses and annotations of those structures available from PDBe. Additionally, CCDC will develop infrastructure to allow access to small-molecule data in the Cambridge Structural Database (CSD) for those compounds that are present in the both the CSD and the PDB. This will facilitate real-time programmatic access to up-to-date information from PDBe databases and advanced tools and services, which will become available to any bioinformatics and structural-biology-workflow systems as well as individual programs. In addition, access to experimentally determined structures from the CSD will provide better quality starting models for ligands during the macromolecular structure determination process. This, in turn, will improve the quality of deposited ligand data in the PDB, benefitting chemoinformatics research and informing the structure-based design of new drugs.In this project, we propose to develop a method to provide access to types of PDBe and CCDC data and information in an integrated framework:1. PDB data from the PDBe database infrastructure2. Advanced analysis and annotations on biomacromolecular assemblies3. Ligand environment and 3D structural motifs data from PDBeMotif4. Up-to-date cross-references for all PDB entries, taken from the SIFTS resource5. Data-quality indicators for all PDB entries6. Access to CSD data for molecules that are also in the PDB