Calculator Plugins

range of structure based prediction tools
Trainable predictions
Take advantage of the tunable physicochemical property predictions, such as pKa or logP.
Valuable descriptors for ADME
Apply ChemAxon’s calculated properties as descriptors in ADME studies.
3D characterization and modeling
Calculation of various geometric descriptors that help 3D characterization of compounds, fast conformer generation, 3D alignment and molecular dynamics.
Apply calculations on molecular files or databases via your preferred desktop application.

ChemAxon’s Calculators and Calculator Plugins

ChemAxon’s Calculators and Calculator Plugin suite is a cheminformatics toolkit built on integrated technologies that achieve unmatched performance and versatility. It offers solutions to a wide range of problems faced by researchers with all levels of modeling expertise. Implemented calculations and property predictions efficiently evaluate pharmaceutically relevant physicochemical properties and molecular descriptors even for hundreds of thousands compounds, making it a powerful lead generation and lead optimization tool.

Physicochemical property predictors

This set of tools offers fast, accurate and trainable predictions of basic physicochemical properties such as logP, logD, pKa. In addition, robust prediction of NMR spectra of molecules that facilitates structure interpretation and elucidation is also available. Besides the predictors, this collection contains the technology to generate stereoisomers and tautomers of the input structures according to user-specified limits. Since a significant fraction of drug-like molecules are weak acids or bases with multiple low-energy ionization or tautomeric states, reliable prediction of these properties is invaluable during pharmaceutical research, or the characterization of various organic and inorganic chemical processes.

Structural property calculations

The molecular property and descriptor calculations allow the evaluation of various topology-related characteristics. These include simple elemental analysis, structural keys, hydrogen bonding and other physical properties, topological polar surface area or molecular surface area descriptors with wide applicability to both biological activity and ADME property prediction. Descriptors can also be used for classification, clustering and filtering of compounds, as well as for predictive model construction.

Molecular Properties Modelling

ChemAxon offers a streamlined interface for interactive molecular mechanics applications such as 3D ligand geometry optimization and the generation of conformation ensembles. The easy-to-use 3D alignment or Molecular Dynamics tools makes it invaluable for both computational and medicinal chemists. Partial charge distribution and its derivatives determine many physicochemical properties of a molecule such as reactivity or pharmacophore patterns.


ChemAxon’s Calculators and Calculator Plugins are available throughout the tool of the JChem technology via command line, the Chemical Terms language and the application programming interface (API). They are also implemented in all our desktop applications, e.g. Marvin, Instant JChem and JChem for Excel. In addition, Calculator Plugins can also be used with popular workflow and analysis applications such as Pipeline Pilot, KNIME, InforSense and Spotfire.

Articles in the library

Chemicalize Webinar - Why Google Isn't Enough for Chemists

Feb 16, 2017 - Webinar
An introduction to Document and Structure Search modules. The benefits of chemically intelligent searches over Google search. An overview of the current available databases and our custom…

Marvin Live at Vertex Pharmaceuticals Incorporated

Sep 14, 2016 - Presentation
We will describe briefly how Marvin Live is used at Vertex Pharmaceuticals Incorporated. We will share our involvement in the early development of Marvin Live.

Chemicalize Webinar - Calculations Property Predictions for All Chemists

Feb 14, 2017 - Webinar
A detailed introduction of the Calculation module and ChemAxon’s chemical predictions behind it. The benefits of property predictions over simple property databases. An overview of the …

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