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).

The three‐dimensional environments of ligand binding sites have been derived from the parsing and loading of the PDB entries into a relational database. For each bound molecule the biological assembly of the quaternary structure has been used to determine all contact residues and a fast interactive search and retrieval system has been developed. Prosite pattern and short sequence search options are available together with a novel graphical query generator for inter‐residue contacts. The database and its query interface are accessible from the Internet through a web server located at: http://www.ebi.ac.uk/msd‐srv/msdsite. Proteins 2005. © 2004 Wiley‐Liss, Inc.

The E-MSD macromolecular structure relational database (http://www.ebi.ac.uk/msd) is designed to be a single access point for protein and nucleic acid structures and related information. The database is derived from Protein Data Bank (PDB) entries. Relational database technologies are used in a comprehensive cleaning procedure to ensure data uniformity across the whole archive. The search database contains an extensive set of derived properties, goodness-of-fit indicators, and links to other EBI databases including InterPro, GO, and SWISS-PROT, together with links to SCOP, CATH, PFAM and PROSITE. A generic search interface is available, coupled with a fast secondary structure domain search tool.

This chapter discusses the use of five model-building applications within the program QUANTA that allow various levels of automation of map interpretation and model (re)-building. It also discusses the use of X-ray applications within the program QUANTA, with particular reference to the Q2002 release. The methods described in the chapter cannot interpret maps that do not contain useful information but come close to the abilities of a competent crystallographer and provide various levels of automation, depending on the quality of the experimental data. The X-ray tools within QUANTA were designed with the goal of reducing the interactive time of the expert crystallographer. With good data, QUANTA makes the process available to the nonexpert. Tools on the main palettes of X-BUILD, X-AUTOFIT, X-SOLVATE, and X-LIGAND are referred to by the tool name. X-LIGAND and X-SOLVATE are applications for the placement of multiple water positions and flexible ligands into electron density. In both applications, a tool (Site search) carries out a peak search within the map, excluding peaks that are too close to the protein or other peaks, symmetry-related peaks, and those below a density threshold. By far, the easiest method of tracing a map is to use the Go button on the X-POWERFIT palette that converts all the currently placed vectors into trace (Tool = X-POWERFIT/Go). This requires no user interaction.