Peter W. Rose, Bojan Beran, Chunxiao Bi, Wolfgang F. Bluhm, Dimitris Dimitropoulos, David S. Goodsell, Andreas Prlić, Martha Quesada, Gregory B. Quinn, John D. Westbrook, Jasmine Young, Benjamin Yukich, Christine Zardecki, Helen M. Berman, Philip E. Bourne

The RCSB Protein Data Bank (RCSB PDB) web site (http://www.pdb.org) has been redesigned to increase usability and to cater to a larger and more diverse user base. This article describes key enhancements and new features that fall into the following categories: (i) query and analysis tools for chemical structure searching, query refinement, tabulation and export of query results; (ii) web site customization and new structure alerts; (iii) pair-wise and representative protein structure alignments; (iv) visualization of large assemblies; (v) integration of structural data with the open access literature and binding affinity data; and (vi) web services and web widgets to facilitate integration of PDB data and tools with other resources. These improvements enable a range of new possibilities to analyze and understand structure data. The next generation of the RCSB PDB web site, as described here, provides a rich resource for research and education.