Abstract
Due to the increasing amount of publicly available protein structures searching, enriching and investigating these data still poses a challenging task. The ProteinsPlus web service (https://proteins.plus) offers a broad range of tools addressing these challenges. The web interface to the tool collection focusing on protein–ligand interactions has been geared towards easy and intuitive access to a large variety of functionality for life scientists. Since our last publication, the ProteinsPlus web service has been extended by additional services as well as it has undergone substantial infrastructural improvements. A keyword search functionality was added on the start page of ProteinsPlus enabling users to work on structures without knowing their PDB code. The tool collection has been augmented by three tools: StructureProfiler validates ligands and active sites using selection criteria of well-established protein–ligand benchmark data sets, WarPP places water molecules in the ligand binding sites of a protein, and METALizer calculates, predicts and scores coordination geometries of metal ions based on surrounding complex atoms. Additionally, all tools provided by ProteinsPlus are available through a REST service enabling the automated integration in structure processing and modeling pipelines.
Highlights
Available structural data of macromolecular complexes in the Protein Data Bank (PDB) [1] are often used as starting point for the successful development of new drugs [2]
Together with the additional functionality described above, ProteinsPlus evolved into a versatile instrument for molecular modeling processes
Further usability improvement of ProteinsPlus workflows could be reached by an increase of tool interoperability: using results from calculations of other tools as input without needing intermediate formatting steps would enable the implementation of automated workflows
Summary
Available structural data of macromolecular complexes in the Protein Data Bank (PDB) [1] are often used as starting point for the successful development of new drugs [2]. We present an extended version of ProteinsPlus that addresses a large variety of molecular modelling tasks covering the following areas: structure quality assessment by EDIA [18] and StructureProfiler [19], structure enrichment by Protoss [20], WarPP [21], METALizer, 2D visualization by PoseView [22], binding site ensemble generation by SIENA [23], protein–protein interface classification by HyPPI and pocket detection and druggability estimation by DoGSiteScorer [24]. The keyword search enables the user to start ProteinsPlus without knowing the PDB code of the structure of interest.
Sign-in/Register to view highlights & summary 
Published Version (
Free)
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call