PROGRAMMING LIBRARIES FOR MOLECULAR MODELING

Szybki TK

Szybki TK is a general purpose optimizer offering both high-level algorithms for structure optimization using various force fields and low-level functions that provide flexibility for dealing with arbitrary functions and coordinate frames.

Supported Force fields in Szybki TK includes OpenFF (Open Force Field Initiative) force fields Sage and Parsley, AMBER Protein force fields ff14SB and AMBER99, and the MMFF94 (Merck Molecular Force Field).

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

Documentation

The OpenEye Toolkit Ecosystem

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
OEMedChem TK Matched molecular pair analysis, fragmentation utilities, and molecular complexity metrics
Saiph TK: Extracting, transforming, and loading (ETL) files and records