Bioisostere TK

Bioisostere TK provides functionalities for bioisosteric analog generation with fragment replacement. It involves replacing a portion of a lead compound with fragments that have similar shape and electrostatics but with potentially novel connectivity and chemistry.

The toolkit centers around fragment-based 3D modeling tools, including fragment creation, fragment conformer generation, fragment alignment, and fragment replacement. Bioisostere TK leverages OpenEye's advanced molecular similarity tools based on shape, chemical features, and electrostatics, and brings those to fragment based modeling.

Bioisostere TK provides level access similar to the existing BROOD and CHOMP applications.

Documentation

Bioisostere TK fragment overlay between a reference and a fit fragment, based on shape and color. The attachment points in both the reference and fit fragments are marked in purple. The fragment overlay highlights how special attention is paid to the overlay of the attachment points.

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
Bioisostere TK Bioisosteric fragment replacement and analog generation

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