PoseView

Overview

PoseView automatically generates 2D diagrams of protein-ligand complexes, focusing on the interactions between protein and ligand. Interactions between molecules are estimated by an underlying interaction mode that relies on atom types and simple geometric criteria. It adheres to the conventions of chemical structure diagram generation. The quality of the resulting diagrams is comparable to manually drawn examples from books and scientific publications.

Method

In a complex diagram, hydrogen bonds are represented as dashed lines, and both the interacting residues of the receptor and atoms of the ligand are depicted as a structure diagram. Spline segments showing hydrophobic regions of the ligand represent hydrophobic contacts between protein and ligand. The coordinates of the structure diagram and their layout modifications are generated by the library SDGlib.[1] The depiction of residues is based on the interaction calculations using the FlexX library.[2] Users can write complex diagrams to a file in PNG, PDF, SVG, or EPS format. Interacting amino acids can be displayed as structure diagrams of complete molecules or of the interacting molecule part.

[1] Fricker, P. C.; Gastreich, M.; Rarey, M. Automated drawing of structural molecular formulas under constraints. J Chem Inf Comput Sci 2004, 44 (3), 1065-1078. DOI: https://doi.org/10.1021/ci049958u
[2] Rarey, M.; Kramer, B.; Lengauer, T.; Klebe, G. A fast flexible docking method using an incremental construction algorithm. J Mol Biol 1996, 261 (3), 470-489. DOI: https://doi.org/10.1006/jmbi.1996.0477

Software Availability

We are offering PoseView as part of our ProteinsPlus web service. Please visit https://proteins.plus, upload your protein-ligand complex, and choose PoseView.

A standalone version of PoseView can be licensed at https://www.biosolveit.de/academic-drug-discovery/#PoseView.

References

Stierand, K.; Rarey, M. Drawing the PDB: Protein-Ligand Complexes in Two Dimensions. ACS Med Chem Lett 2010, 1 (9), 540-545. DOI: https://doi.org/10.1021/ml100164p
Stierand, K.; Rarey, M. From modeling to medicinal chemistry: automatic generation of two-dimensional complex diagrams. ChemMedChem 2007, 2 (6), 853-860. DOI: https://doi.org/10.1002/cmdc.200700010
Stierand, K.; Maass, P. C.; Rarey, M. Molecular complexes at a glance: automated generation of two-dimensional complex diagrams. Bioinformatics 2006, 22 (14), 1710-1716. DOI: https://doi.org/10.1093/bioinformatics/btl150

Example