VISUALIZATION OF MOLECULAR INTERACTIONS & PROPERTIES

Grapheme™ TK

2D structure depiction of molecules is the "natural language" of chemists, since this representation instantly conveys many important molecular properties.

Historically, 2D representations have mainly been used to visualize the connection table of molecular graphs. However, projecting 3D information into the 2D layout and displaying various atom and bond properties on the molecular diagram opens up a novel way to present information to chemists.

Grapheme TK provides several representation schemes that allow visualization of complex molecular interactions and properties in a clear and coherent 2D format that is the most natural to chemists.

Molecule annotations: (a) visualizing atom partial charges (b) annotating rotatable bonds.

Fig. 2 Visualizing the B-factor of the ligand (MOA) using atom annotations and projecting the average B-factor of the adjacent receptor atoms into the 2D molecule surface (complex 1meh). Fig. 3 Projecting the contribution of each atom of the total OEXLogP into a 2D property map.

Features

Wide range of built-in atom and bond glyphs for annotation
Molecule surface
Property map
2D coordinates generation driven by 3D conformation
Visualizing ligand-protein complex surface

Generation of 2D depictions (a) default 2D layout, (b) 3D conformation, (c) 2D layout driven by 3D conformation.

Example of the 2w3a complex (a) in VIDA (b) the 2D depiction of the complex where the molecule surface is annotated based on the distance between the accessible surfaces of the ligand and the surrounding protein.

For more detailed information on Grapheme TK, check out the link below:

Documentation

Cheminformatics

The Cheminformatics suite of toolkits provides the core foundation upon which all the OpenEye applications and remaining toolkits are built.

OEChem TK Core chemistry handling and representation as well as molecule file I/O
OEDepict TK 2D Molecule rendering and depiction
Grapheme™ TK Advanced molecule rendering and report generation
GraphSim TK 2D molecular similarity (e.g. fingerprints)
Lexichem TK name-to-structure, structure-to-name, foreign language translation
MolProp TK Molecular property calculation and filtering
Quacpac TK Tautomer enumeration and charge assignment
MedChem TK Matched molecular pair analysis, fragmentation utilities, and molecular complexity metrics

Modeling

The Modeling suite of toolkits provides the core functionality underlying OpenEye's defining principle that shape & electrostatics are the two fundamental descriptors determining intermolecular interactions. Many of the toolkits in the Modeling suite are directly associated with specific OpenEye applications and can, therefore, be used to create new or extend existing functionality associated with those applications.

OEChem TK Core chemistry handling and representation as well as molecule file I/O
FastROCS™ TK Real-time shape similarity for virtual screening, lead hopping & shape clustering
OEDocking TK Molecular docking and scoring
Omega TK Conformer generation
Shape TK 3D shape description, optimization, and overlap
SiteHopper TK Rapid Comparison of Protein Binding Sites
Spicoli TK Surface generation, manipulation, and interrogation
Spruce TK Protein preparation and modeling
Szybki TK General purpose optimization with MMFF94
Szmap TK Understanding water interactions in a binding site
Zap TK Calculate Poisson-Boltzmann electrostatic potentials