PoseView

advantages of using PoseView

• visualize protein-ligand complexes in 2D
• automatically generate publication-quality graphics
• export to a variety of graphics formats

PoseView automatically generates high-quality 2D structure-diagrams of protein-ligand complexes provided as 3D-input. Such input may come directly from crystal structures or be computed for example by a docking program.

The 2D depiction shows hydrogen bonds as dashed lines between the interaction partners on either side. Hydrophobic interactions are illustrated as smooth contour lines between the respective amino acids and the ligand. The ligand itself is drawn utilizing the 2Ddraw engine according to chemical drawing conventions.

To get a deeper insight into the underlying machinery and the scientific challenges hidden by an easy-to-use front end, please visit poseview.zbh.uni-hamburg.de and/or consult the original scientific publications:

• Katrin Stierand and Matthias Rarey
  From Modeling to Medicinal Chemistry: Automatic Generation of Two-Dimensional Complex Diagrams
  ChemMedChem (2007), 2, 853 – 860.
• Katrin Stierand and Matthias Rarey
  Drawing the PDB: Protein-Ligand Complexes in Two Dimensions
  ACS Medicinal Chemistry Letters (2010); DOI: 10.1021/ml100164p

features

• The input can be provided as raw PDB or the FlexX-specific RDF-notation. Ligands need to be provided as mol2-files.
• The output can be visualized in a GUI or exported to PNG-, PDF- or XFIG files. The latter providing the opportunity to modify the graphic in the full-featured graphics program XFIG.
• Various display options can be chosen, such as show/hide of interaction energies, show/hide hydrophobic contacts, as well as several labelling options.
• PoseView may be used on the command-line for high-throughput processing of multiple data, or via an intuitive graphical user-interface.

future directions

PoseView is integrated in LeadIT. Scientifically PoseView will be further developed at the Center for Bioinformatics (ZBH) of the University of Hamburg. It is now available in version 1.1.2.

download

BioSolveIT is proud to contribute PoseView as a community service. The RCSB PDB now uses PoseView to provide to its users 2D images of the macromolecule-ligand complexes on the Structure Summary page. You may also want to test the PoseView web-service of the ZBH.