ChemBio3D Ultra 14.0 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 ChemBio3D Version 14.0

  • Set up Autodock runs to dock flexible ligands into receptors of known 3D shape and compare the goodness of fit
  • Set up CONFLEX® runs to quickly explore conformational space and identify minimum energy conformations for small and large molecules

(W = Windows Only)

ChemBio3D v13 fig1

Figure 1: Chemists and biologists can explore the three dimensional shapes and properties of small molecules and biochemicals at their desktop

ChemBio3D ultra v13 fig2

Figure 2: Visualizing the Binding Site and Surface of a Protein


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, calculation of pKa, LogD and LogS, a new biopolymer toolbar and the ability to read and write a wide variety of chemical file formats including spectra and reactions and to paste amino acid, DNA and RNA sequences.
  • 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.
  • 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.
  • 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.
  • 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.
    ChemBio3D Ultra provides a graphical interface to the GAMESS program for ab initio quantum chemistry. 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.
  • 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.
  • 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.
  • MOPAC 2009 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.
  • 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.
  • 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.

Applications Features

(W) – Feature available on Win only

ChemDraw Pro

  • ActiveX Edit in ChemDraw
    Edit your document using your installed version of ChemDraw, rather than your ActiveX, providing greater screen real estate for editing, and also access to the full range of ChemDraw capabilities.
  • Arrow Tool
    Control every aspect of arrows drawn, including arc, length, headstyle, dipole, no-go and more.
  • Chain Tool
    Draw both acyclic and snaking chains.
  • Chemical File Format
    Reading & writing of chemical file formats including skc, mol v3000, sdf, spectra & reactions.
  • Chemical Warnings
    Mouse-over red box to read error description.
  • ChemProp
    (W) Advanced property parameter including BP, MP and more.
  • Custom Templates & Nicknames
    Ability to create & edit templates & nicknames.
  • Expand Generic Structure
    Generate multiple structures from an “abbreviated” generic structure.
  • Floating Character Map
    Add special characters from any font instantly to any ChemDraw document.
  • Floating Periodic Table
    Element information available at all times with floating periodic table on the desktop.
  • Freehand Drawing Tool
    Use the mouse or other pointing device to draw freehand shapes using this intuitive drawing tool.
  • Gel Electrophoresis Plate Tool
    Draw gel electrophoresis plates. This new tool is similar to TLC Plate Tool, and provides arbitrary rotation for lane labels, drag and position band labels, paste data from Excel or other sources, and copy and paste between lanes.
  • I/Draw Mode
    New compatibility mode allows ChemDraw to look and feel like your legacy drawing package.
  • ISIS-style Data SGroups
    Data can be attached to objects.
  • LabArt
    Publication-quality EPS glassware art for use within your ChemDraw documents.
  • Mass & Other Fragmentation Tools
    Three fragmentation tools: Mass, Dissociation, & Retrosynthesis.
  • MS Office Integration
    (W) ChemDraw offers full integration via OLE, so you can embed your drawings in any Office document.
  • Multi-Page Docs
    Create multiple page documents and posters within a single ChemDraw file.
  • Name>Struct/Excel
    (W) Generate a ChemDraw structure in MS Excel by typing in systematic chemical names for most substances.
  • Online Menu
    (W) Draw a structure or model and immediately get online vendor information ChemACX.Com with the click of a button.
  • Polymer Draw
    Represent and manipulate polymers in ChemDraw.
  • Properties HotLink
    Chemical names, formulas, molecular weights, and other physical properties added to the document are “live”, and will now update automatically as modifications are made to structural diagrams.
  • Relative Stereochemistry
    Allows specification of relationships between groups of stereocenters smaller than an entire molecule.
  • Stereochemistry
    Identifies stereocenters using Cahn-Ingold Prelog rules.
  • Structure CleanUp
    Improves poor drawings.
  • Structure Perspective Tool
    Adjust the perspective of ChemDraw molecules with simple horizontal/vertical mouse movements.
  • Terminal Carbon Labeling
    Automatic display of atom labels on terminal carbon atoms.
  • TLC Plate Tool
    Draw thin layer chromatography plates. Drag plate to size and drag spots to required positions. Shape and color spots and set or display Rf values.
  • tPSA
    Topological Polar Surface Area (tPSA) provides a fast approximation of the molecular polar surface area, a useful parameter for prediction of drug transport properties, which has been show to correlate with human intestinal absorption and blood-brain barrier penetration.

ChemBio3D Ultra

  • 3D Glasses
    (W) Included glasses provide enhanced stereo-mode with depth shadings to give realistic 3-dimensional quality to all Chem3D renderings. (Included in CD-ROM purchases only.)
  • Automatic Overlay
    (W) Select multiple molecules and let Chem3D automatically align them with a target molecule.
  • ChemDraw HotLink
    (W) Simultaneous 2D & 3D editing! Draw structures using a ChemDraw window embedded in the Chem3D application. This powerful feature adds a 2D view that is always in-sync with the 3D view.
  • ChemProp
    (W) Advanced property parameter including BP, MP and more.
  • CLogP
    (W) CLogP property server provides the latest methodology for calculationg n-octanol/water partition coefficients.
  • Dihedral Driver
    (W) New conformational analysis tool allows the generation of MM2 energy plots.
  • Enhanced Graphics
    (W) Chem3D uses openGL to provide high quality graphics display.
  • Formal Charges
    (W) Assign Formal Charges to Atoms and Chem3D will generate delocalised charges automatically.
  • GAMESS Interface
    (W) Chem3D interface to GAMESS.
  • Group Labels
    (W) Display group labels in the Chem3D model view.
  • Hydrogen Bonds
    (W) Automatically display hydrogen bonds in the 3D view!
  • Kekule / Delocalised Display Mode
    (W) Toggle between dashed line and alternating single-double bond representation of delocalised and aromatic bonds.
  • LogD
    Calculate the logarithmic value of the distribution coefficient D, which is the ratio of the sum of the concentrations of all forms of the compound (ionized plus un-ionized) in each of the two phases.
  • LogS
    Calculate the logarithmic value of the aqueous solubility S of a compound. This value significantly affects its absorption and distribution characteristics.
  • MM2
    (W) Built in support for MM2 to generate realistic 3D structures.
  • MMFF94
    (W) MMFF94 is a molecular mechanics force-field that supports both organic molecules and biopolymers. MMFF94 force field provides a richer set of atom types than MM2. Enable multiprocessor support in MMFF94 calculations.
  • Model Explorer
    (W) Hierarchical tree-control for exploring the structure of large models. Import a PDB file and examine chains, groups, and ligands. This new feature gives fine-grained control.
  • Molecular Modeling & Dynamics
    (W) Workstation quality molecular modeling.
  • MOPAC Interface
    (W) Chem3D interface to MOPAC. (Note: MOPAC application is required. See applications included section to clarify.)
  • Multiprocessor Support
    Enable multiprocessor support in MMFF94 calculations.
  • Partial Surfaces
    (W) Generate and display partial surfaces for protein active sites.
  • pKa
    Calculate the logarithmic value of the acid dissociation constant Ka, which is a quantitative measure of the strength of an acid in solution.
  • PowerPoint
    (W) Embed Chem3D models in PowerPoint files. Rotate and zoom Chem3D models while giving a presentation.
  • Save to Dropbox
    Use Cloud storage via Dropbox to save, share and import ChemBio3D models in a secure but sharable Cloud location.
  • Schrödinger Jaguar Interface
    (W) Chem3D interface to Schrödinger Jaguar, an ab-initio calculation package. (Note: Jaguar application is required. See applications included section to clarify.)
  • Spectrum Viewer
    (W) Display spectral calculation results from Jaguar, Gaussian, and GAMESS as a graphical display in a separate window.
  • Stochastic Conformational Analysis
    Determination of low-energy minima of a molecule using a stochastic conformational jump procedure.
  • Structure Browser
    (W) Allows users to easily scroll through a collection of small molecules and compare their structures and properties.

ChemBioFinder Std

  • ActiveX Control Boxes
    (W) Include third party ActiveX controls on your form.
  • Automatic Form Generation
    (W) Automatically build or extend databases by importing structures from collections of structure files, databases, SDFiles, or other sources.
  • ChemBioFinder/Office
    (W) Search on your computer or network for chemical structures in Word, Excel, Powerpoint, ChemDraw, ISIS files and more, and browse, search, refine, or export your hit list to any destination.
  • Chemical Searching
    (W) Search for (sub)structure, similarity, numeric values, text, chemical formula (including element ranges, element exclusions), date. Support for tautomers and alt groups.
  • Hit List and Query Management
    (W) Use a navigation tree to track history of searches between sessions, allow queries to be rerun or reconstituted; merge lists by drag-and-drop in tree. Queries color-coded to relate to ChemBioViz plots.
  • List Merge
    (W) Merge hitlists with any logic: intersect, union, subtract, reverse subtract.
  • Multiple Data Views
    (W) View records one at a time, in a table view or a multiform view.
  • Scripting
    (W) Python scripts can be written to automate the application and can be attached to buttons on the form or to database trigger events. User the enhanced Script Editor to develop and debug — now featuring interactive line-by-line execution — and display output in a new dockable text window. CAL is a simple programming language, accessible to non-programmers allows automation, self-running demos, custom operations; includes debugging features.
  • Standardized Handling of Implict Hydrogens
    Conforms to industry standards.
  • Subforms
    (W) Link relational data to your main table via subforms.
  • Tabbed Forms
    (W) Partition a form into sections using tabbed form pages.

ChemDraw/Excel Pro

  • ChemDraw/Excel
    (W) Use Excel to organize and analyze your chemical data.
  • Name=Struct/Excel
    (W) Generate a ChemDraw structure in MS Excel by typing in systematic chemical names for most substances.

ChemScript Pro

  • ChemScript Pro
    Apply chemical business rules to chemical objects by using customizable scripts

Gaussian Interface

  • Gaussian Interface
    (W) Chem3D interface to Gaussian.
    (Note: Gaussian application is required. See applications included section to clarify.)


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