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About ProteinsPlus

The aim of ProteinsPlus is to support life scientists in working with protein structures. Protein structures are the key for an understanding of function. They are an important resource in many biotechnological application areas from pharmaceutical research to biocatalysis. ProteinsPlus has its focus on protein-ligand interactions. The server provides support for the initial steps when dealing with protein structures, namely structure search, preprocessing and quality assessment. All tools are developed in the Computational Molecular Design Group (AMD) headed by Matthias Rarey. Currently, ProteinsPlus allows you to:

  • Visualize structures and create 2D pose depictions (PoseView)

  • Predict protonation and tautomerization, place hydrogen atoms (Protoss)

  • Generate SMILES notations for small molecules in PDB files

  • Predict binding sites and estimate their druggability (DoGSiteScorer)

  • Search for alternative binding site models and conformations and generate aligned protein structure ensembles (SIENA)

  • Measure and visualize electron density support for individual atoms and structural units (EDIA)

  • Classify the interaction type of protein-protein complexes (HyPPI)

Several of the underlying tools are components of professional molecular modeling software provided by BioSolveIT GmbH. Some tools are available as part of the AMD software collection for stand-alone use in academic and commercial environments from us.

The development of the ProteinsPlus web service is supported by the BMBF as part of de.NBI – German Network for Bioinformatics Infrastructure. Its use is free for academic and commercial purposes – we thank you for citing the computational methods behind ProteinsPlus. You find the corresponding references in the short description of each tool.


ProteinsPlus is a common framework to make computational tools for structure- based molecular design developed in the AMD research group of Prof. Matthias Rarey available on the web. The usage of this service is free of charge. We thank you for citing the computational methods behind ProteinsPlus. You find the corresponding references in the short description of each tool. For more information on scientific literature, software availability, and projects we refer to our group homepage and to the web page of our software development partner BioSolveIT.

The ProteinsPlus server and all its attached components are provided as is. Any warranties, including, but not limited to correctness, fitness for a particular purpose, data safety are disclaimed. In no event, the University of Hamburg shall be liable for any direct or indirect damages.


The server uses the following technology:
- Ruby On Rails: rubyonrails.org
- NGL Viewer: github.com/arose/ngl

We thank all developers for generously providing this software.

We are happy to receive feedback and comments, please contact us via e-mail at pplus(at)zbh.uni-hamburg.de.

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