JChem for Office

enabling chemistry in Microsoft Office

JChem for Office integrates structure handling and visualizing capabilities within a Microsoft Office environment. The bundle includes JChem for Excel which is our long-standing Excel integration. With JChem for Office, chemistry is made live in your Office application and structures are fully supported within spreadsheets, documents, slides and e-mails. Implementation is robust with fast loading/scrolling of many thousands of structure rows and copy-paste throughout the Microsoft Office suite. More advanced functionality includes: structure based calculations, R-group decomposition and library enumeration.

Product Type:application
Interfaces:GUI ( Desktop )API ( .NET )

JChem for Office

Live chemical structures throughout Office

JChem for Office provides a wide integration with MS Office that allows you to enrich Office documents with chemical structures and calculations. Structures can be easily loaded and edited making it easier to prepare reports and calculate properties on spreadsheets.

JChem for Office without license

Word documents, PowerPoint slides and e-mail sent from Outlook which are created using JChem for Office can be read by a colleague without installing JChem for Office. Excel files with structures and JChem for Excel functions can also be read without license but does require installing JChem for Office. More details »

Copy and paste across MS Office

Using ChemAxon software you can copy structures to any Office application. Furthermore, if you use Excel conditional formatting, then this is also carried forward when you paste into you PowerPoint or Word document.

Connections to other applications

JChem for Office works well together with other ChemAxon products. If you are using Instant JChem (enterprise license), then a bridge is used to pass selections and projects into Office documents. There are also KNIME nodes and Pipeline Pilot components to handle JChem for Excel workbooks in batch mode.

Import and Export Structures

Flexible file import and export

JChem for Office has versatile file import and export capabilities, recognizing the standard chemical file formats (sdf, rdf, IUPAC name, smiles, mrv) and being able to handle even large sets, i.e. thousands of rows of chemical and non-chemical data can be easily imported, managed and scrolled.


Extract structures from documents

ChemAxon’s Document to Structure technology is deeply integrated, allowing you to extract chemical names and structures from documents into your Excel sheet as live structures. It supports PDF, TXT, HTML, XML, MS Office documents (DOC, DOCX, PPT, PPTX, XLS, XLSX), OpenOffice ODT, etc.

Additional Import Capabilities in Excel

Import from various databases

Rounding out the capabilities, JChem for Excel can connect to different database engines such as Oracle or MySQL. Importing from database allows filtering through structure and data searches so only a pre-filtered data-set is imported into the Excel sheet, and not the complete database.

Supported database engines in JChem for Excel

Associate IDs with structures

Compounds are commonly referred by their internal compound IDs, however chemists want to see the actual structures. If you have compound IDs on your sheet the structures they refer to can be retrieved from your corporate structure. Compound IDs also can be associated during file import process.

Extending Excel Features with Chemistry

JChem for Excel functions

A key feature of JChem for Excel is the degree of integration of our structure based calculations (Calculator Plugins) within Excel’s custom functions. With the JChem for Excel functions, users can populate columns with physicochemical properties, molecular descriptors and topology analysis results. Various indices used in drug discovery are also implemented such as Lipinski drug-likeness. Chemical Terms, a language for combining and extending Calculator Plugins is also natively integrated, letting users easily set up complex structure based arguments to populate cells.

Another benefit of the deep integration is that adding new rows or editing structures automatically updating dependent columns.

JChem for Excel functions

Structure searches

It is possible to filter structures from the active worksheet. You can search for structures by a query structure and specified search options. Similarity, substructure, full structure, superstructure and duplicate searches are directly available in JChem for Excel. It is possible to apply further structure filtering to narrow the hit list. Chemical data-sets can be easily divided and selected rows exported into standard chemical files that can be further processed by other applications.

Supporting Medicinal Chemistry

Compound profiling

Compound profiling in JChem for Excel

Having JChem’s chemistry resolution available within Excel functions compound profiling can be done easily. Structure-based data generated by JChem for Excel functions and experimental data can be brought together, statistically analyzed and visualized by the Excel functions and charts. Radar charts can be used to help the visual characterization of a smaller set of compounds, and also can be used for presentation purposes. Similarity indices can also facilitate the identification of similar or dissimilar clusters.

Structure similarity matrix

Structure-Activity Relationship table generation

R-group decomposition is a frequently used approach to generate either Markush tables providing input for virtual library generators; or Structure-Activity Relationship (SAR) tables that are often used during the drug development phases. R-group decomposition is a special kind of substructure search that aims to find a central structure, or scaffold, and identify its substituents at certain attachment positions. The query molecule consists of the scaffold and ligand attachment points represented by R-groups. These R-groups are simple R-group atoms without R-group definitions in most cases. The resulting R-group table can further be characterized using the JChem for Excel functions together with the Excel functions; frequently occurring substituents and their contributions to the biological activity can be statistically evaluated.

R-group in JChem for Excel


Competitor analysis is one of the major processes during drug discovery. Researchers can investigate a smaller set of patent IUPAC names which can be imported directly and will automatically be converted into structures, then further characterized. IUPAC names can also be generated for existing data-sets which can be used in the patent application. Read more about Naming »

Virtual library generation

JChem for Excel uses ChemAxon’s Reactor, synthesis engine for virtual library generation. The Reactor engine is available via a simple JChem for Excel function in a single Excel sheet. The general reaction and the reactants are given either in the same sheet or even in different Excel workbooks. Reagents can be arranged in a sequential or combinatorial mode. Products or the whole reaction can be visualized. ChemAxon’s empirical smart rules are available in JChem for Excel, predicting the reactivity and selectivity and can be specified by the user through a generic reaction. For more about generating generic reactions see reaction rules.

ChemAxon’s enumeration technology allows applying empirical smart rules in JChem for Excel, predicting the reactivity and selectivity and practically ensuring synthetic feasibility. Reactivity rules are Boolean expressions describing natural conditions – these conditions should be satisfied, otherwise the reaction does not take place. Selectivity rules are real-valued chemical expressions that order products according to their occurrence.

Supported Office versions

Supported Office versions in JChem for Office

Articles in the library

Development of Compounds Targeting Resistant Cancer – Experiences with Ple…

May 11, 2017 - Presentation
Our research interests focus on compounds that have the potential to overcome multidrug resistance in cancer. Compounds showing paradoxical toxicity against otherwise multidrug resistant …

Enterprise Deployment of JChem for Excel (JC4XL)

Sep 27, 2011 - Presentation
Life scientists have found Microsoft Excel to be an invaluable tool in managing and visualizing research data. ChemAxon’s JChem for Excel (JC4XL) enhances Excel’s capabilities by incl…

Excel as a Cheminformatics Interface

Sep 28, 2011 - Presentation
Commercial add‐in programs introduce chemical intelligence into Excel, therefore enable Excel to become a serious development platform candidate for Cheminformatics applications. We wil…

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