Molecular complexes at a glance: automated generation of two-dimensional complex diagrams.
BACKGROUND
In this paper a new algorithmic approach is presented, which automatically generates structure diagrams of molecular complexes. A complex diagram contains the ligand, the amino acids of the protein interacting with the ligand and the hydrophilic interactions schematized as dashed lines between the corresponding atoms. The algorithm is based on a combinatorial optimization strategy which solves parts of the layout problem non-heuristically. The depicted molecules are represented as structure diagrams according to the chemical nomenclature. Due to the frequent usage of complex diagrams in the scientific literature as well as in text books dealing with structural biology, biochemistry and medicinal chemistry, the new algorithm is a key element for computer applications in these areas.


RESULTS
The method was implemented in the new software tool PoseView. It was tested on a representative dataset containing 305 protein-ligand complexes in total from the Brookhaven Protein Data Bank. PoseView was able to find collision-free layouts for more than three quarters of all complexes. In the following the layout generation algorithm is presented and, additional to the statistical results, representative test cases demonstrating the challenges of the layout generation will be discussed.


BACKGROUND
The method is available as a webservice at http://www.zbh.uni-hamburg.de/poseview.
Stierand
Katrin
K
Center for Bioinformatics (ZBH), University of Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany.
Maass
Patrick C
PC
Rarey
Matthias
M
D000465:Algorithms; D001665:Binding Sites; D003198:Computer Simulation; D008024:Ligands; D008956:Models, Chemical; D008958:Models, Molecular; D046912:Multiprotein Complexes / Q000032:analysis / Q000737:chemistry* / Q000648:ultrastructure; D011485:Protein Binding; D011487:Protein Conformation; D011506:Proteins / Q000032:analysis / Q000737:chemistry* / Q000648:ultrastructure; D020539:Sequence Analysis, Protein / Q000379:methods*; D014584:User-Computer Interface
D008024:Ligands; D046912:Multiprotein Complexes; D011506:Proteins