MarvinSketch

Advanced chemical editor for drawing chemical structures, queries and reactions

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.

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

Chemical structure drawing

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.

Reaction Drawing

Query drawing

Atom lists, bond lists, not lists, generic atoms, R-groups, and 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.

Query Drawing

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 integrated NMR Predictor 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, the generation of fast and accurate or most likely structures is useful.

Calculators

Molecular descriptors

Marvin uses the following to calculate molecular descriptors: 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. Marvin users can calculate partial charge distribution and its derivatives which determine many phyiscochemical properties of a molecule such as reactivity and pharmacophore pattern.

Molecular Modeling

Chemical feature parade

Welcome to the widest support for chemical structure file formats

In addition to all popular 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

MarvinSketch supports 3D editing and cleaning on the canvas. Adjustable 3D transformations and display of degree of rotation with specific axis can easily be performed. Directed merge feature allows you to connect a selected fragment to another fragment according to assigned atom pairs helping draw large molecules or peptides accurately.

Molecule and structure 3D manipulations

Structure and Valence checker

ChemAxon’s Structure Checker technology is used to check and fix erroneous features in chemical structure files when importing files. Structure Checker checks and automatically fixes structures while you draw in Marvin. 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.

Structure and valance checker

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 the 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. 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.

Chemical template library

Search ChemSpider and PubChem databases via MarvinSketch

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

Search ChemSpider and PubChem database

Reporting and Publishing

Image generation, display and formatting

MarvinSketch supports various molecule display and formatting options to generate high quality structure images for reporting or publication purposes. Marvin is able to export bitmap image files like JPEG, MS BMP, PNG, PPM and vector graphics files like SVG, PDF and EMF. Through the style tools and included template styles you can quickly reformat your molecules for specific journal styles.

Chemical drawer display and formatting

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 directly in Microsoft documents and presentations.

Chemical Structure

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 users in their everyday sketching.

Template Library

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.

Articles in the library

CzeekD: Fragment-based de novo Drug Design System for Drug Discovery

Sep 26, 2014 - Presentation
It has been estimated that there is an enormous number of compounds that consist the vast chemical space and as such, the use of an optimal method to search for novel active compounds is …

Challenges and Approach in Migration of Chemistry Infrastructure for Systems…

Sep 25, 2014 - Presentation
Chemistry infrastructure serves as a backbone of pharmaceutical discovery informatics. In last two year, we have implemented and migrated most of our applications and systems using ChemAx…

A chemistry friendly system integrating drug design tools and a consistent v…

Sep 26, 2014 - Presentation
Drug discovery today is challenging with metabolism and toxicity playing key roles. Here we present a web based system created at Cubist to allows scientist to use QSAR models and other c…
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