What does the proteins plus tool suite do?
Water molecules and metal ions play a key role in the mediation of protein–ligand interactions. Therefore, the Proteins Plus tool suite has been augmented by a water placement procedure (WarPP) ( 21) and a metal complex geometry prediction tool (METALizer).
Is proteins plus free for commercial use?
Some tools within Proteins Plus are available for download within the NAOMI ChemBio Suite. The suite is available free of charge for academic use only. The authors declare financial conflict of interest in case that the NAOMI ChemBio Suite is licensed to commercial users for charge.
What's new in proteins plus?
Most noteworthy, a keyword search, interactive pocket definition and handling, and a REST API have been implemented. The keyword search enables the user to start Proteins Plus without knowing the PDB code of the structure of interest.
What is the entry point to proteins Plus service?
The entry point to the Proteins Plus service is in many cases a publicly available structure from the PDB whose PDB code is not necessarily known to the user. To overcome this issue, a keyword search combined with a small number of quality filters was introduced.
Abstract
Due to the increasing amount of publicly available protein structures searching, enriching and investigating these data still poses a challenging task. The Proteins Plus web service ( https://proteins.plus) offers a broad range of tools addressing these challenges.
INTRODUCTION
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 ).
SUMMARY AND OUTLOOK
Together with the additional functionality described above, Proteins Plus evolved into a versatile instrument for molecular modeling processes. The analysis and processing of binding sites and ligands on atomic level give comprehensive insights in the binding mode of the interacting molecules.
FUNDING
Development of Proteins Plus by de.NBI (in part); German Federal Ministry of Education and Research (BMBF) [031L0105]. Funding for open access charge: German Federal Ministry of Education and Research (BMBF) [031L0105].
Notes
Present address: Eva Nittinger, Medicinal Chemistry, Respiratory Inflammation and Autoimmune (RIA), BioPharmaceutical R&D, AstraZeneca, Gothenburg, Sweden; Ruben Steinegger, IT, Perfood GmbH, Lübeck 23564, Germany.
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