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Toolkit Development Platform

Programming Libraries for Creating Custom Applications, Scripts and Web Services

The OpenEye toolkits are programming libraries, commonly called software development kits (SDKs), for creating custom applications, scripts and/or web services. All of the toolkits are developed in C++ to ensure exceptional performance but are also available to developers in Python, Java, and .NET for maximum flexibility and utility. Each toolkit has its own well documented and stable API with extensive examples. The toolkits are broadly categorized into two major suites: Cheminformatics and Modeling.

Supported Platforms

After several failed attempts with open source software, I resorted to a commercial solution. The best tool I found for parsing XYZ files and assigning bond orders was the OEChem toolkit from OpenEye Scientific Software. Using OEChem, I could parse the XYZ files and correctly assign bond orders. - Pat Walters, Practical Cheminformatics

2025.1 Applications and Toolkits

NEW SCIENCE and IMPROVED USABILITY

FastROCS: Grid Query Support
FastROCS TK now supports grid-based shape queries, expanding the types of queries inputs to include active site negative images, composite queries combining grids and molecules, and queries derived from crystallographic density.
Bioisostere TK: Feature Extensions
All capabilities previously available in the BROOD application are now integrated into Bioisostere TK. Users can design more selective and synthetically accessible bioisosteres by incorporating both on-target and off-target (selectivity) proteins into their queries, enabling more informed replacement suggestions. The toolkit also supports fragment bridging for macrocyclization and performs availability checks against commercial and internal databases, saving time and resources.
SZYBKI: Robust Protein–Ligand Optimization
SZYBKI and Szybki TK now provide more robust protein–ligand optimization, significantly lowering minimization failure rates. Streamlined ligand charge assignment and integration with OEDocking and/or POSIT allow users to optimize more structures with greater efficiency.
And much more.

OpenEye Toolkits are a suite of high-performance software development kits designed for scientific computing, particularly in cheminformatics and molecular modeling. It widely used in pharmaceutical and drug discovery research due to its flexibility, speed, and accuracy.

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 Force field based focused optimization and Entropy estimations
OEFF TK Force fields and general optimization tools
Szmap TK Understanding water interactions in a binding site
Zap TK Calculate Poisson-Boltzmann electrostatic potentials
Bioisostere TK 3D fragment similarity, lead optimization, and analog generation
Eon TK Molecular shape and electrostatic overlap

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