With currently more than 126 000 publicly available structures and an
increasing growth rate, the Protein Data Bank constitutes a rich data source
for structure-driven research in fields like drug discovery, crop science and
biotechnology in general. Typical workflows in these areas involve manifold
computational tools for the analysis and prediction of molecular functions.
Here, we present the ProteinsPlus web server that offers a unified easy-to-use
interface to a broad range of tools for the early phase of structure-based
molecular modeling. This includes solutions for commonly required pre-
processing tasks like structure quality assessment (EDIA), hydrogen placement
(Protoss) and the search for alternative conformations (SIENA). Beyond that,
it also addresses frequent problems as the generation of 2D-interaction
diagrams (PoseView), protein–protein interface classification (HyPPI) as well
as automatic pocket detection and druggablity assessment (DoGSiteScorer). The
unified ProteinsPlus interface covering all featured approaches provides
various facilities for intuitive input and result visualization, case-specific
parameterization and download options for further processing. Moreover, its
generalized workflow allows the user a quick familiarization with the
different tools. ProteinsPlus also stores the calculated results temporarily
for future request and thus facilitates convenient result communication and
re-access. The server is freely available at http://proteins.plus