2D depiction of protein-ligand complexes.
A method is presented for the automated preparation of schematic diagrams for protein-ligand complexes, in which the ligand is displayed in conventional 2D form, and the interactions to and between the residues in its vicinity are summarized in a concise and information-rich manner. The structural entities are arranged to maximize aesthetic ideals and to properly convey important distance relationships. The diagram is annotated with calculated hydrogen bonds, a substitution contour, solvent exposure, chelated metals, covalently bound linkages, pi-pi and pi-cation interactions, and, for series of complexes, conserved residues and interactions. Residues, cofactors, ions, and solvent components are drawn in cartoon form as adjuncts to the ligand. The method can be applied to aligned sets which contain multiple ligands, or multiple members of a protein family, in which case the ligand orientations and protein residue placement will show consistent trends throughout the series.
Clark
Alex M
AM
Chemical Computing Group, Inc., 1010 Sherbrooke Street West, Suite 910, Montréal, Québec, Canada H3A 2R7. aclark@chemcomp.com
Labute
Paul
P
D015106:3',5'-Cyclic-GMP Phosphodiesterases / Q000037:antagonists & inhibitors; D000465:Algorithms; D002412:Cations / Q000737:chemistry; D002614:Chelating Agents / Q000737:chemistry; D054706:Cyclic Nucleotide Phosphodiesterases, Type 5; D018844:Cyclin-Dependent Kinases / Q000037:antagonists & inhibitors; D016208:Databases, Factual; D006860:Hydrogen Bonding; D008024:Ligands; D008670:Metals / Q000737:chemistry; D008958:Models, Molecular; D008968:Molecular Conformation; D010726:Phosphodiesterase Inhibitors / Q000737:chemistry / Q000494:pharmacology; D011506:Proteins / Q000737:chemistry*; D011955:Receptors, Drug / Q000737:chemistry / Q000187:drug effects; D012997:Solvents
D002412:Cations; D002614:Chelating Agents; D008024:Ligands; D008670:Metals; D010726:Phosphodiesterase Inhibitors; D011506:Proteins; D011955:Receptors, Drug; D012997:Solvents; D018844:Cyclin-Dependent Kinases; D015106:3',5'-Cyclic-GMP Phosphodiesterases; D054706:Cyclic Nucleotide Phosphodiesterases, Type 5