TOOLKIT DEVELOPMENT PLATFORM

MolProp TK

The MolProp TK provides a customizable framework for molecular property calculation geared towards enabling rapid database filtering. Filtering attempts to eliminate inappropriate or undesirable compounds from a large set before beginning to use them in modelling studies.

The goal is to remove all of the compounds that should not be suggested to a medicinal chemist as a potential hit. This exercise is obviously case dependent, depending on ease of the assay, intended target, personal bias of the modeller & medicinal chemist, strengths of the company, etc., which makes this problem one that is highly amenable to a toolkit solution.

Example of OpenEye’s molecular property calculation implemented as a workflow solution in Orion® for extremely fast database filtering

Readily available molecular properties calculation

The criteria for passing or failing a given molecule fall into three categories:

Physical properties

Molecular weight
Topological polar surface area (TPSA)
logP
Bioavailability

Atomic and functional group content

Absolute and relative content of heteroatoms
Limits on a very wide variety of functional groups

Molecular graph topology

Number and size of ring systems
Flexibility of the molecule
Size and shape of non-ring chains

Beyond the standard molecular properties available from OEChem TK such as molecular weight and atom type counts, MolProp TK calculates XlogP [1], XlogS, and PSA [2]. There is also a variety of ADME filters available such as Lipinski [3], Egan [4], Veber [5] and Martin [6].

In addition to calculating properties and filtering on those properties, MolProp TK provides a variety of preprocessing tools for metal and salt removal, pKa normalization, normalization, reagent selection and type checking.

For more detailed information on MolProp 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