JChem for Excel

Flexible import from standard files

JChem for Excel has strong file import 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.

Customisable import from 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 therefore only a pre-filtered dataset is imported into the Excel sheet.

JChem for Excel as a viewer

Working with live structures

Live chemical objects can be added and edited with just a click using the native MarvinSketch editor or other standard chemical editors such as ChemDraw or ISIS/Symyx Draw. Structures are correctly represented within Excel, interacting with Excel functions and automatically updating associated calculated data. Live objects can also be converted to smiles strings, images or Marvin OLE shape objects for distributing or storing Excel files.

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. Directly from Excel’s functions users can populate columns with physico-chemical 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 updated dependent columns.

Customisable display and structure rendering

JChem for Excel features extensive visualization options, users can set rendering and display options not only for chemical structures but reactions, complexes or polymers. In addition to the usual options more advanced visualization settings for stereochemistry features, rendering options, atom or bond properties are available.

Structure images

Live chemical structures can simply be converted into images by using JChem for Excel functions. Rough description of molecules often helps the intuitive research; analyses of atomic contributions to LogP, pKa, polarizability, refractivity, Huckel analysis or partial charge calculations can serve valuable information on the synthetic feasibility, binding affinity or orientation.

JChem for Excel image functions were developed to visualize Rendering options, Display options and Calculator Plugins results.

Standardization

Standardizer is a structure canonicalization tool for converting molecules from different sources into standard representational forms and could be considered as allowing building of chemical business rules. Standardizer can automate the identification of mesomers, tautomers, stereoisomers and counter-ion removal. Aromatization or cleaning can also be automatically applied. Using the standardizer JChem for Excel function helps users to store and visualize the structures in a pre-defined way e.g. for further presentations purposes.

Compound profiling

Having the advantage that JChem for Excel technology interacts with Excel functions, compound profiling can be done easily. Structure-based data generated by JChem for Excel functions and experimental data can easily be 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 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 sequentially to narrow the hit list. Chemical datasets can be easily divided and selected rows exported into standard chemical files that can be further processed by other applications.

R-group decomposition supporting 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. It is a special kind of substructure search that aims at finding a central structure – 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.

Fast 2D/3D cleaning

Often imported structures do not look correct or are dissimilar to structures already in the worksheet. Users can clean structures easily either in 2D or 3D directly from the menu. The calculation generates acceptable 3D structures and conformers of a given molecule. The 3D structure (conformation) strongly affects the properties and the reactions of molecules, so a medicinal chemist can have a first quick estimation in Excel about the 3D representation which often has an intuitive value during research.

Naming

Competitor analysis is one of the major steps 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 datasets which can be used in the patent application.

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 reaction see Reactor rules.

ChemAxon’s enumeration technology allows applying empirical smart rules in JChem for Excel, predicting the reactivity and selectivity. 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.