Ensemble

ChemBio3D Ultra 14 Suite

The ChemBio3D® Ultra 14.0 suite brings workstation-quality molecular graphics and rigorous computational methods to your desktop, allowing you to explore the structure and properties of large chemical and biological models. The Structure Browser enables viewing sets of small structures and their properties for analysis and comparison.

Highlights in Version 14.0

  • Set up AutoDock runs to dock flexible ligands into receptors of known 3D shape and compare the goodness of fit
    • "I have just run AutoDock using the default ligand and am amazed at the results… the ChemBio3D interface is markedly easy to use… the speed of execution, albeit for a rather small molecule is the fastest I've seen in a MS OS. Well done!"
      Stephen Molnar Ph.D., Foundation for Chemistry
    Visualizing the Binding Site and Surface of a Protein.

    Figure 2: Visualizing the Binding Site and Surface of a Protein.
    [Click picture to enlarge]

  • Set up CONFLEX® runs to quickly explore conformational space and identify minimum energy conformations for small and large molecules

For more information on all of the applications that are include in the ChemBio3D Ultra suite, please see the Applications tab below.

Chemists and biologists can explore the three dimensional shapes and properties of small molecules and biochemicals at their desktop.

Figure 1: Chemists and biologists can explore the three dimensional shapes and properties of small molecules and biochemicals at their desktop
[Click picture to enlarge]

Applications

Applications Included
ChemDraw Pro
In addition to basic chemical structure drawing, this premier application provides chemical query properties, the ability to create and edit templates and nicknames, annotation, relative stereochemistry, ISIS/Draw Compatibility, support for ISIS-style Data SGroups, chemical file formats, expansion of generic structures, TLC and Gel Electrophoresis Plate Tools, freehand pen tool, fragmentation tools, PolymerDraw, ChemProp, structure clean-up, and the ability to read and write a wide variety of chemical file formats including spectra and reactions.
ChemBio3D Ultra
This ultimate application for desktop molecular modeling and state-of-the-art protein visualization is designed for chemists and biologists. Visualize detailed 3D protein-ligand complexes and DNA structures using open GL graphics and stereo hardware and display and analyze Hydrogen bonds and partial surfaces. Build small molecules using the ChemDraw interface and see the 3D structure appear simultaneously, perform basic Molecular modeling computations such as Alignment, Stochastic conformational sampling, Dihedral driver, MM2 experiments, Molecular Mechanics with support for MMFF94.and Dynamics. Perform ab initio and semi-empirical calculations, and predict and visualize NMR, IR and Raman spectra with interfaces to MOPAC, Jaguar, GAMESS, Gaussian, and, new in 13.0, Autodock and CONFLEX for flexible ligand docking and conformational analysis.

* Windows Only

ChemBioFinder Std
ChemBioFinder Std is a database management system for anyone who works with chemical information and chemical structure databases. Browse, create, search, and update databases with structural, numeric, and text data via user-customizable forms, including structural and sub-structural queries, as well as linking to related data in sub-forms. View and edit structures in a variety of modes, automatically create databases and forms for imported data, export and print.

* Windows Only

ChemDraw/Excel Pro
ChemDraw/Excel allows scientists to create chemically intelligent spreadsheets within the familiar Microsoft Excel environment. Build and manipulate chemical structures within Excel, compute chemical properties and use structure and substructure searches to locate and group compounds.

* Windows Only

ChemBioFinder for Office
ChemBioFinder for Office locates and searches structure files contained in documents on your computer or network drives. Multiple structure file types are recognized, including cdx, mol, sdf, rxn and skc, and search results can be displayed or exported as SDfiles.

* Windows Only

ChemScript Pro
ChemScript allows scientists to perform multiple calculations or manipulations on chemical structures in batch mode, up to 10,000 operations per day. Enforce structure orientation, perform template-based normalization, salt-stripping, generate canonical codes (molecular fingerprints), and convert file formats.

* Windows Only

MOPAC Interface for ChemBio3D
MOPAC is a general-purpose semi-empirical quantum mechanics package for the study of chemical properties and reactions in gas, solution, or solid-state. This premier molecular computation application features a number of widely-used, semi-empirical methods and allows you to compute properties and perform energy minimizations, optimize to transition states, and compute properties. It supports MOPAC sparkles, has an improved user interface, and provides faster calculations.

* Windows Only

Autodock
ChemBio3D Ultra provides a graphical interface to the Autodock suite of automated docking tools, which is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. This enables researchers to examine and compare the docking of flexible ligands to receptors via a user interface that steps through the process in in logical and simple steps.

* Windows Only

GAMESS and GAMESS Pro Interface
ChemBio3D Ultra provides the GAMESS program for ab initio quantum chemistry and includes a graphical interface to GAMESS. A variety of wavefunctions (RHF, ROHF, UHF, GVB, and MCSCF, CI and MP2 energy corrections) and basis sets are available. Users can also calculate vibrational frequencies and a variety of molecular properties, such as dipole moments, hyperpolarizabilities. GAMESS is maintained by the members of the Gordon research group at Iowa State University.

* Windows Only

CONFLEX Interface
ChemBio3D Ultra provides a graphical user interface to the CONFLEX program for high performance conformational analysis and energy minimization of small and large molecules. CONFLEX can completely search the conformational space of a flexible molecule to find every optimal structure of chemically significant conformers.

* Windows Only

Gaussian Interface
Gaussian is a series of electronic structure programs used by chemists, chemical engineers, biochemists, physicists and other scientists worldwide. Starting from the fundamental laws of quantum mechanics, Gaussian predicts the energies, molecular structures, vibrational frequencies and molecular properties of molecules and reactions in a wide variety of chemical environments.

* Windows Only

Features

Applications Features

(W) - Feature available on Win only

ChemDraw Pro

ActiveX Edit in ChemDraw Arrows Tool View demo clips of this feature Chain Tools View demo clips of this feature Chemical File Format View demo clips of this feature Chemical Warnings View demo clips of this feature ChemProp View demo clips of this feature Custom Templates & Nicknames View demo clips of this feature Expand Generic Structure View demo clips of this feature Floating Character Map View demo clips of this feature Floating Periodic Table View demo clips of this feature Freehand Drawing Tool Gel Electrophoresis Plate Tool I/Draw Mode View demo clips of this feature ISIS-style Data SGroups LabArt View demo clips of this feature Mass & Other Fragmentation Tools View demo clips of this feature MS Office Integration Multi-Page Docs View demo clips of this feature Online Menu Polymer Draw View demo clips of this feature Properties HotLink View demo clips of this feature Relative Stereochemistry View demo clips of this feature Stereochemistry View demo clips of this feature Structure CleanUp Structure Perspective Tool TLC Plate Tool View demo clips of this feature tPSA

ChemDraw ActiveX/Plugin Pro 13.0

ActiveX Edit in ChemDraw Arrows Tool View demo clips of this feature Chain Tools View demo clips of this feature Chemical File Format View demo clips of this feature Chemical Warnings View demo clips of this feature Custom Templates & Nicknames View demo clips of this feature Expand Generic Structure View demo clips of this feature Floating Character Map View demo clips of this feature Floating Periodic Table View demo clips of this feature Freehand Drawing Tool I/Draw Mode View demo clips of this feature ISIS-style Data SGroups LabArt View demo clips of this feature Mass & Other Fragmentation Tools View demo clips of this feature MS Office Integration Multi-Page Docs View demo clips of this feature Online Menu Polymer Draw View demo clips of this feature Properties HotLink View demo clips of this feature Relative Stereochemistry View demo clips of this feature Stereochemistry View demo clips of this feature Structure CleanUp Structure Perspective Tool TLC Plate Tool View demo clips of this feature tPSA

ChemBio3D Ultra

3D Glasses View demo clips of this feature Automatic Overlay View demo clips of this feature ChemDraw HotLink View demo clips of this feature ChemProp View demo clips of this feature CLogP Dihedral Driver View demo clips of this feature Enhanced Graphics View demo clips of this feature Formal Charges GAMESS Interface View demo clips of this feature Group Labels Hydrogen Bonds View demo clips of this feature Kekule / Delocalized Display Mode LogP LogS MM2 View demo clips of this feature MMFF94 View demo clips of this feature Model Explorer View demo clips of this feature Molecular Modeling & Dynamics MOPAC Interface View demo clips of this feature Partial Surfaces View demo clips of this feature pKa PowerPoint View demo clips of this feature Save to Dropbox Spectrum Viewer Stochastic Conformational Analysis Structure Browser

ChemBioFinder Std

ActiveX Control Boxes View demo clips of this feature Automatic Form Generation ChemBioFinder/Office Chemical Searching View demo clips of this feature Hit List and Query Management View demo clips of this feature List Merge View demo clips of this feature Multiple Data Views View demo clips of this feature Scripting View demo clips of this feature Standardized Handling of Implict Hydrogens Subforms Tabbed Forms

ChemDraw/Excel Pro

ChemScript Pro

ChemScript Pro View demo clips of this feature

Gaussian Interface

Gaussian Interface