Toolkit Development Platform

Grapheme™ TK

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.

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

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


 Documentation   >   Evaluate

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

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

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.

Cheminformatics

The Cheminformatics suite of toolkits provides the core foundation upon which all of the OpenEye applications and remaining toolkits are built. The Cheminformatics suite is a collection of seven individual yet interdependent toolkits that are described in the table below.

  Toolkit Major Functionality
  FastROCS TK Real-time shape similarity for virtual screening, lead hopping & shape clustering
  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.

  Toolkit Major Functionality
  OEChem TK Core chemistry handling and representation as well as molecule file I/O
  OEDocking TK Molecular docking and scoring
  Omega TK Conformer generation
  Shape TK 3D shape description, optimization, and overlap
  Spicoli TK Surface generation, manipulation, and interrogation
  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
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