Proteins Plus Logo

About ProteinsPlus

The aim of ProteinsPlus is to support life scientists in working with protein structures 1. 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)2

  • Predict protonation and tautomerization, place hydrogen atoms (Protoss)3,4

  • Generate SMILES notations for small molecules in PDB files8,9

  • Predict binding sites and estimate their druggability (DoGSiteScorer)5

  • Search for alternative binding site models and conformations and generate aligned protein structure ensembles (SIENA)6,10

  • Measure and visualize electron density support for individual atoms and structural units (EDIA)7

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

  • Prediction of coordinates of metals in metalloproteins (METALizer)

  • Screening of structures based on selection criteria (StructureProfiler)

  • Find structural data of the PDB to activity values stored in the ChEMBL database (ActivityFinder)

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 ProteinsPlus and the computational methods behind it. You find the corresponding references below and 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. 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. Everybody from the AMD group provided components in use behind ProteinsPlus. The ProteinsPlus web server was originally developed by Rainer Fährrolfes. Many thanks to Ruben Steinegger who developed the keyword search functionality on top of the PDB RESTful service (Bachelor thesis at the Technische Hochschule Mittelhessen (THM)).

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.

To justify funding for our web services, we are obliged to collect statistical information about their usage. The package Matomo is applied to gather the following user information in an anonymous form:

  • anonymised ip address
  • web browser and plugins
  • operating system
In case you want to use our tools without tracking of any kind, we encourage you to install software components locally. Software licenses are provided free of charge for academic use (see http://software.zbh.uni-hamburg.de for further information).


The server uses the following technology:
- Ruby On Rails: rubyonrails.org
- NGL Viewer: github.com/arose/ngl
- Chart.js: github.com/chartjs/Chart.js
- Moment.js: github.com/moment/moment
- DataTables: datatables.net
- Bootstrap: getbootstrap.com
- DelayedJob: github.com/collectiveidea/delayed_job_active_record
- Paperclip: github.com/thoughtbot/paperclip
- D3: Data-Driven Documents: d3js.org
- Matomo: matomo.org
- The RCSB PDB RESTful Web Service interface: rcsb.org

We thank all developers for generously providing this software.


References

[1] Fährrolfes, R.; Bietz, S.; Flachsenberg, F.; Meyder, A.; Nittinger, E.; Otto, T.; Volkamer, A.; Rarey, M. (2017). ProteinsPlus: a web portal for structure analysis of macromolecules. Nucleic Acids Research, 45:W337-W343.
[2] Stierand, K., Maaß, P., Rarey, M. (2006) Molecular Complexes at a Glance: Automated Generation of two-dimensional Complex Diagrams. Bioinformatics, 22, 1710-1716.
[3] Lippert, T., Rarey, M.: Fast automated placement of polar hydrogen atoms in protein-ligand complexes. Journal of Cheminformatics 2009, 1:13
[4] Bietz, S., Urbaczek, S., Schulz, B., Rarey, M.: Protoss: a holistic approach to predict tautomers and protonation states in protein-ligand complexes. Journal of Cheminformatics 2014, 6:12.
[5] A. Volkamer, D. Kuhn, T. Grombacher, F. Rippmann, M. Rarey. Combining global and local measures for structure-based druggability predictions. J. Chem. Inf. Model. 2012,52,360-372.
[6] Bietz, S.; Rarey, M. (2016). SIENA: Efficient Compilation of Selective Protein Binding Site Ensembles. Journal of Chemical Information and Modeling, 56 (1), pp 248–259.
[7] Meyder, A.; Nittinger, E.; Lange, G.; Klein, R.; Rarey, M. (2017). Estimating Electron Density Support for Individual Atoms and Molecular Fragments in X-ray Structures. Journal of Chemical Information and Modeling, 57(10): 2437–2447.
[8] Hilbig, M., Urbaczek, S., Groth, I., Heuser, S., & Rarey, M. (2013). MONA–Interactive manipulation of molecule collections. Journal of cheminformatics, 5(1), 38.
[9] Hilbig, M.; Rarey, M. (2015). MONA 2: a light cheminformatics platform for interactive compound library processing. Journal of Chemical Information and Modeling. 55 (10), 2071-2078.
[10] Bietz, S.; Rarey, M. (2015). ASCONA: Rapid Detection and Alignment of Protein Binding Site Conformations. Journal of Chemical Information and Modeling 55 (8), 1747-1756.

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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