Ligand (biochemistry)

Maximum bubble pressure method

Receptor

Service (business)

Protein Data Bank (RCSB PDB)

Biology

Protein ligand

Operating system

Interface (matter)

Protein Data Bank

Geodesy

World Wide Web

Engineering

Bubble

Economy

Benchmark (surveying)

Artificial intelligence

Economics

Systems engineering

Geography

Computer science

Task (project management)

Protein structure

Computational biology

User interface

Web service

Biochemistry

Database

Selection (genetic algorithm)

Application programming interface

Nucleic Acids Research

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.

ProteinsPlus: interactive analysis of protein–ligand binding interfaces