PoseView

The software tool PoseView [1] automatically creates two-dimensional diagrams of complexes with known 3D structure according to chemical drawing conventions.



Complex of Estrogen Receptor Alpha and Diethylstilbesterol. PDB code: 3erd.



Excluded Ligands
Diagram description
Directed bonds between protein and ligand are drawn as dashed lines and the interacting protein residues and the ligand are visualized as structure diagrams. Hydrophobic contacts are represented more indirectly by means of spline sections highlighting the hydrophobic parts of the ligand and the label of the contacting amino acid. The generation of structure diagrams and their layout modifications are based on the library 2Ddraw [2]. Interactions between the molecules are estimated by a builtin interaction model that is based on atom types and simple geometric criteria.
Features of the standalone version
- Complex diagrams can be shown in a browser or written to a file in one of the following formats: PNG, PDF, SVG or EPS.
- Interacting amino acids can be displayed as structure diagrams of complete molecules or of the interacting molecule part.
- Hydrogen bonds can be labeled by their energy or length.
- Hydrophobic contacts can be hidden.
- PoseView is available as standalone tool and integrated in the LeadIT platform at http://www.biosolveit.de/poseview.

Related Publications
[4] Stierand, K., Rarey, M. (2010) Drawing the PDB: Protein−Ligand Complexes in Two Dimensions. Medicinal Chemistry Letters, 1 (9), 540-545.

[3] Stierand, K., Rarey, M. (2007) From Modeling to Medicinal Chemistry: Automatic Generation of Two-Dimensional Complex Diagrams. ChemMedChem 2 (6), 853-860.

[2] Fricker, P., Gastreich, M., and Rarey, M. (2004) Automated Generation of Structural Molecular Formulas under Constraints. Journal of Chemical Information and Computer Sciences, 44, 1065-1078.

[1] Stierand, K., Maaß, P., Rarey, M. (2006) Molecular Complexes at a Glance: Automated Generation of two-dimensional Complex Diagrams. Bioinformatics, 22, 1710-1716.

Funding

The PoseView project is funded by the Klaus Tschira Stiftung gemeinnützige GmbH.