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Computational Toxicology Research Program

SDF Viewers, Structure Browsers & CRD Applications

DSSTox SDF data files are standardized structure-inclusive files (More on SDF) that are designed to be viewed and/or searched within a chemical structure-enable search application. We classify such applications as one of 3 types:

blue bullet graphic SDF Viewers - Freeware
PC-based applications that are primarily designed for viewing the structure and data content of SDF files. These applications may have some limited text/data search capability but do not support structure, substructure, or similarity searching.

blue bullet graphic CRD Applications
Chemical Relational Database Applications can be PC-based or server-based and offer the fullest functionality with respect to searching or mining of structure-data content. CRDs are distinguished from SDF viewers by offering both SDF viewing capability and structure browsing capability, as well as Boolean or relational searching of supplemental data content. See also More on CRDs.

blue bullet graphic Online Structure Browsers Developer Tools
Online structure-enabled search interfaces, with an interactive chemical drawing applet that serves as the front-end for searching on-line, remote, or server-based databases with chemical structure content. These structure browsers may query databases containing only chemical structure content (i.e., no supplemental data), or they may offer more sophisticated relational or Boolean exit EPA searching queries of supplemental data content.


Additional Sources for Chemical Software & Datasets:

blue bullet graphic Chemoinformatics Wikipedia exit EPA

blue bullet graphic QSAR World exit EPA

blue bullet graphic ChemBioGrid: Chemistry Resources on the Web exit EPA

blue bullet graphic SourceForge.net: Chemistry Development Kit exit EPA

blue bullet graphic General Interest Links

Listed below are links to some external websites of public resources, as well as commercial vendors and other suppliers of SDF Viewers, Structure Browsers, and CRD applications. This is a partial list of known products and is not intended to be exhaustive. Information on this page is provided as a courtesy to the user community; however, neither the EPA nor the DSSTox project endorses any CRD product over any other (see additional Disclaimers). Sites that offer freeware products or free trial versions of software are specially marked below. See also Known Problems & Fixes for listing of known problems and fixes encountered with some freeware and commercial software in the course of the DSSTox Project.

Note: In the listing below, a link to the site home page is followed by a link to the specific product page, which is likely to change more frequently. If the url for the specific product page no longer works, users are advised to visit the home page for redirection.

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SDF Structure Viewers - Freeware (novice to experienced users) exit EPA

PowerMV {Freeware}
PowerMV is a PC-based Windows desktop application that can be freely dowloaded and used to import, view, edit, print and export SDF files. Application also offers statistical analysis, dynamic molecular viewing, descriptor generation, and similarity search analysis. Application is easy to use and allows text searching in data fields, but does not allow explicit structure or substructure searching. Developed by Stan Young and collaborators at the National Institute of Statistical Sciences (NISS); no user help manual provided.

Hyleos {Freeware}
Hyleos ChemFileBrowser is a PC-based Windows desktop application that can be freely downloaded and used to import, view, edit, print and export SDF files. Application allows viewing of SDF records with chemical structures and has several useful features, but offers no structure or text searching capabilities.

For a large list of available resources, see Chemoinformatics Wikipedia. See also On-line Structure Browser Developer Tools for links to providers that offer a free non-commercial license for their products when used on public non-profit websites. Also, note, that a number of Commercial CRD Applications vendors offer Free Trial versions of their software.

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CRD Applications (novice to experienced users) exit EPA
Each of these commercial CRD products imports SDF files and each includes or is bundled with a structure-drawing capabiliy for entering structure and search information.

Accelrys, Inc.
Under Accord product listing, find PC/Windows CRD products, Accord for Excel {Free Trial Version}, and the Oracle server-based product, Accord for Oracle.

Advanced Chemistry Development, Inc.
PC/Windows CRD product, ACD/Labs ChemFolder {Free Trial Version}, also includes ACD/ChemSketch; in lieu of a free demo version, provides free on-line training. Note that a scaled down version of the ACD/ChemSketch product (not including the Dictionary) is offered for free, unlimited download and use. The latter includes new features such as InChI code generation and eMolecules site searching.

AMBIT: Software for Data Management & (Q)SAR Applications
Newly developed web-based and stand-alone database and functional modules, built on open source technology and CML compliant, will be fully publicly available. See recent AMBIT presentation for latest update. {Free Non-commercial License}

Bio-Rad Laboratories, Inc., Informatics Division
PC/Windows CRD product, Bio-Rad KnowItAll Informatics System, includes structure drawing and handling of properties for the ADME\Tox user.

CambridgeSoft Corp.
PC/Windows CambridgeSoft ChemOffice Suite {Free Trial Version}, includes CRD ChemFinder, ChemDraw, and Chem3D products. A lower cost option for CRD capability is the ChemDraw Ultra {Free Trial Version} product , which contains fully functional versions of ChemFinder and ChemDraw.

CheD Basic Version
PC/Windows CRD product {Free Trial Version}, with enhancement modules for additional handling of spectral data.

MDL Information Systems, Inc.
Full ISIS product listing under MDL Discovery Framework, includes PC/Windows CRD product, MDL ISIS for Excel, and server-based MDL ISIS/Host and desktop client MDL ISIS/Base.

PC/Windows CRD product, Molsearch Pro, includes structure editor.

PC/Windows and Unix bioinformatics analysis suite includes a ChemoInformatics CRD module for managing chemical, structural and biological data.

Supported on Windows, Linux, Mac OSX, and IRIX systems, VIDA is a sophisticated graphical interface browser designed to visualize, manage and manipulate large sets of molecular information.

For larger lists of available resources, see Additional Sources for Chemical Software & Datasets.

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On-line Structure Browser Developer Tools (experienced programmers) exit EPA

For experienced programmers, offers downloadable, pre-compiled CACTVS Tools written in UNIX, including a 2D structure browser and editor and www substructure search tool kit; serves as structure-search engine for NCI Structure Browser. {Free Non-commercial License}

ChemAxon Ltd.
For the experienced website developer, offers downloadable Java tools for creating intranet or internet structure-drawing capabilities, using Marvin, and CRD searching capabilities using JChemBase. {Free Non-commercial License}

A relatively new public resource (June 2007) , offers free on-line searchability through >16 million compounds. Can be accessed from within a user website using ChemSpider html code with embedded chemical text search (name, InChI, SMILES, etc).

Originally known as "Chmoogle", this public structure-browsing locator site allows users to Upload a Catalog of Chemicals (SD File) for free access and browsing within their on-line system across an inventory of more than 7 million compounds.

Editor for drawing 2D chemicals structures developed by an international team of open-source programmers, distributed through the open-source distributor, SourceForge.net. Ref: Krause, Stefan, Willighagen, Egon, and Steinbeck, Christoph. "JChemPaint - Using the Collaborative Forces of the Internet to Develop a Free Editor for 2D Chemical Structures". 2000. 93-98. 5. It can be read from http://www.mdpi.org/molecules/html/50100093.htm. {Free Non-commercial License}

Molinspiration Cheminformatics
Web-based molecular database and property prediction platform-independent toolkits written in Java (see products pg), including the misearch toolkit, a flexible molecular database, supporting substructure, similarity and pharmacophore similarity searches.

For additional resources, see also Chemoinformatics Wikipedia.

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