MarvinSketch

Easy chemical structure, query and reaction drawing

Chemical structure drawing

MarvinSketch allows users to quickly draw molecules through basic functions on the GUI and advanced functionalities such as sprout drawing, customizable shortcuts, abbreviated groups, default and user defined templates and context sensitive popup menus.

Atom and Bond properties

MarvinSketch has a rich support for atom and bond properties. Users can assign stereochemistry, charge, valence, radicals and isotopes to each atom. Single, double, triple bonds and aromatic forms are supported. Moreover using wedge bonds user can assign stereochemistry to atoms. Additional data fields can also be attached to atoms, via “S-group” logic so that any user defined information can be stored directly with the structural information.

Reaction drawing

You can draw single step reactions in MarvinSketch by placing a reaction arrow in any position, pointing in any direction in relation to reaction products. The structures ‘in front’ of the arrow will be recognized as reactants, structures ‘above’ the arrow as agents, and structures behind as products. Atoms can be automatically or manually mapped using the arrow function.

Query drawing

Atom lists, bond lists, not lists, generic atoms, R-groups, lone pairs are among the query building features available in MarvinSketch. Link nodes, repeating units, pseudo atoms and homology groups, S-groups with attached data are also supported. SMARTS rules allow users to define any specific or generic queries.

Bringing the power of ChemAxon’s Calculator Plugin technology directly onto the canvas

Tune, combine and view

Calculator Plugins offer a solution to a wide range of problems faced by medicinal or computational chemists. ChemAxon’s Calculator Plugin suite is a cheminformatics toolkit to calculate structure based properties and gives unmatched versatility and power in characterizing your structures. Through Chemical Terms, a language to parameterize and combine Calculator Plugin results, you can quickly see a range of relevant properties and arguments for the structure or structures on the canvas as you are creating.

Predictors and Enumerators

ChemAxon’s software offers fast and accurate predictions of basic physicochemical properties such as logP, logD, pKa. Furthermore, ChemAxon’s NMR Predictor is integrated that can play an important role in structure validation and elucidation of molecules. It now considers novel coupling types and improved accuracy. Multiple stereoisomers and tautomers of each input structure can also be generated 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, fast and accurate or most likely structures is useful.

Molecular descriptors

Calculating molecular descriptors include; topological indices, structural keys, indices, 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, filtering and predictive model construction.

Molecular Modeling

ChemAxon offers a streamlined interface for interactive molecular mechanics applications such as 3D ligand optimization and conformation generation. Intuitive and fast 3D alignment and Molecular Dynamics control makes it invaluable for both computational and medicinal chemists. Partial charge distribution and its derivatives determine many physico-chemical properties of a molecule such as reactivity or pharmacophore pattern and can called from the interface.

Chemical feature parade

Welcome to the widest support for chemical structure file formats

In addition to most chemical file formats MarvinSketch can open protein, nucleic acid sequence files, Gaussian input and output files, chemical name file formats, JChem Table files. ChemDraw and Symyx Draw file formats (skc, cdx) are also recognized by Marvin. In the IP space Marvin users can also import Markush DARC files and save all features within Marvin’s default (mrv) format for sharing and subsequent editing. Marvin can import and export single and multiple molecules. Structures from image files can be converted in MarvinSketch using the free OSRA application.

3D manipulations

In addition to most chemical file formats MarvinSketch can open protein, nucleic acid sequence files, Gaussian input and output files, chemical name file formats, JChem Table files. ChemDraw and Symyx Draw file formats (skc, cdx) are also recognized by Marvin. In the IP space Marvin users can also import Markush DARC files and save all features within Marvin’s default (mrv) format for sharing and subsequent editing. Marvin can import and export single and multiple molecules. Structures from image files can be converted in MarvinSketch using the free OSRA application.

Structure and Valence checker

ChemAxon’s Structure Checker technology is used to check and fix erroneous features in chemical structure files during import or file open. Structure Checker is extensively integrated within Marvin so checking and automatically fixing structures while you draw. Structure checker can automatically run a customisable list of fixers and either warn or correct found errors. In semi manual mode a separate window opens taking you through a range of possible fixes that can be applied automatically.

Working with abbreviated groups

MarvinSketch provides a range of standard pre-defined abbreviated groups which can be placed on the drawing cursor just by typing the first characters of their name. On canvas lists let you navigate and explore options and users can define, name and store custom abbreviated groups to quickly refine and work more quickly with the types of molecules you are routinely working with.

Markush structure sketching and representation

MarvinSketch allows users to easily sketch Markush structures or import Thomson Reuters Markush DARC file formats. The ChemAxon’s new representation follows the IUPAC representation.

Working with built-in and user defined template libraries

MarvinSketch provides several predefined chemical structure categories within the template library, including; amino acids, cycloalkaynes, polycyclics, and many more. For ease of use, the template toolbar can be brought onto the MarvinSketch interface so you can drag and drop structures from the library to the canvas. Users can define their own templates in various ways, including by dragging a structure from the canvas to the templates toolbar.

Search ChemSpider and PubChem databases via MarvinSketch

Several online database searches can accessed directly from MarvinSketch. Users can execute substructure, similarity or superstructure searches.

Working with chemical structures in Microsoft Office

Chemical structures can be saved as image files and inserted in Microsoft Office files. Marvin Objects (OLE) are also supported enabling work with chemical structures in Microsoft documents and presentations.

Usability

Clear and customizable interface – See only what you want to see

You can easily personalize the MarvinSketch user interface to better suit your needs or style, even choose to configure layout to resemble other chemical editors, such as ChemDraw or ISISDraw, including their shortcut rules. For example, you can reorganize the menu bar contents and order or create new menu bars. Any changes you make will be stored as your default next time you open Marvin Sketch. Scaling molecules is enabled via setting the bond length and size of objects. Furthermore, an extensive and continuously growing template library is helping the users in their everyday work.

Batch calculations and file format conversion using MolConverter

MolConverter is a command line program in Marvin Beans and JChem that converts between various file types. Operating in batch mode users can specify various documents, molecule files, graphic and compression/encoding formats. When handling chemical structures users can specify how to handle chemical features relevant to molecule file formats. Converting structures to CAS numbers in a batch mode has never been easier.

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