Ensemble

ChemBioOffice Ultra 14 Suite

ChemBioOffice® Ultra 14.0 provides biologists and chemists with an up-to-date suite of scientifically intelligent applications for increased personal productivity and enhanced decision-making.

For more information on all of the applications that are included with ChemBioOffice Ultra 14.0, please click on the Applications tab below

Highlights in Version 14.0

The following are highlights of the features in ChemBioOffice Ultra 14.0. For a full list of ChemBioOffice features, please click on the Features tab below.

"The Biopolymer Toolbar is a huge help to draw peptides or DNA sequences. It is easy to handle and saves a lot of time."
    Dr. Richard J. Smith, Associate Editor, Verlag Helvetica Chimica Acta
"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
"ChemBioFinder has been invaluable in keeping track of large databases of molecules"
    Stephen Molnar Ph.D., Foundation for Chemistry
Personal productivity tools to organize and explore compounds, reactions, materials and associated properties.

Figure 1: Personal productivity tools to organize and explore compounds, reactions, materials and associated properties.
[Click picture to enlarge]

ChemBioDraw® - Scientifically Intelligent Drawing Tools

  • Search SciFinder direct from ChemBioDraw Ultra with no time-consuming cutting and pasting
  • Cut and paste CDXML and molfile text to and from the clipboard to allow exchange of data with other applications that can read these formats.
  • Biopolymer toolbar with disulfide and lactam bridges, beta and D-amino acids, DNA, RNA,protecting groups and linkers
  • Paste peptide, DNA and RNA sequences and have them interpreted chemically with sequence wrapping and shaping
  • Gel Electrophoresis Plate Tool provides arbitrary rotation for lane labels, drag and position band labels, paste data from Excel or other sources, and copy and paste between lanes
  • Calculators for pKa, LogP and LogS enable scientists to explore important bioavailability properties such acid dissociation, distribution and aqueous solubility for putative compounds

ChemBio3D® - Molecular Graphics and Computational Methods

  • Use ChemBio3D to 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

ChemBioFinder™ - Database Management and Search

  • A chemically and biologically intelligent database manager and search engine
  • Cluster analysis helps scientists discover similarities within sets of compounds and properties.

Applications

Applications Included
ChemBioDraw Ultra

This ultimate chemistry and biology drawing application delivers all of the industry leading drawing, publishing and analytical features in ChemDraw, including direct searching in SciFinder, combined with the biology features in BioDraw, providing a complete solution for chemical structure drawing and analysis combined with biological pathway drawing.

ChemBioDraw Ultra now includes a direct link to search SciFinder. Chemical structure analysis tools include 13C and 1H NMR prediction with peak splitting and highlighting and choice of solvent, Struct=Name, ChemDraw/Excel, stoichiometric analysis, property predictions including pKa*, LogP and LogS* live-linked to the structure, a live-linked Database Gateway, fragmentation tools, TLC and Gel Electrophoresis plate drawing tools, and 3D structures live-linked to the 2D structure.

ChemBioDraw also offers customization options for Nicknames, Templates, and HotKeys. The biopolymer toolbar enables creation of peptide, DNA and RNA sequences, including beta and D-amino acids, disulfide and lactam bridges and linkers and protecting groups. Biological pathway drawing elements include membranes, DNA, enzymes, receptors, and reaction arrows. tRNA, Ribosomes, Helix Proteins, Golgi Bodies, G-Proteins, Immunoglobins, Mitochondrion, new Freehand Pen Tool, Annotation, and a Plasmid mapping tool are also included.

* Windows only.

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 Ultra
ChemBioFinder Ultra is the ultimate database management system for chemical structure and information databases. Browse, create, search, and update local databases with structural, numeric, and text data via user-customizable forms, including structural, sub-structural, and similarity queries, as well as linking to related data in sub-forms. Calculate values for physical properties, view and edit structures in a variety of modes, automatically create databases and forms for imported data, export and print. Easily manage saved queries, access favorite databases, and view database structure via the dockable Explorer Window. Features include the ability to perform RGroup Analysis, read graphic files from the database, Python programming and improved tautomeric searching.

* Windows Only

ChemBioViz Pro

ChemBioViz Pro is a rich toolkit for visualizing numeric data in ChemBioFinder. Calculate and display structure activity relationships, clustering relationships, and statistical data, including histograms, scatter, logarithmic plots, and dendrograms. Descriptive statistics include minimum, maximum, mean, median, standard deviation and more. Create Compound Profiles and visually compare and rank structures based on values of selected properties and the cost profile associated with each property. Create plots within ChemBioFinder sub-forms.

ChemBioViz is a visualization application which works with ChemBioFinder Ultra and allows users to correlate biological activity with chemical structures. ChemBioViz transforms ChemBioFinder data into easy to understand graphics, allowing scientists to easily discern structure-activity relationships. ChemBioViz generates an interactive window containing a variety of plot types and allows researchers to analyze data using a variety of statistical analytical tools. Users can then filter their data on any field in the database in order to examine subsets of data in order to locate trends and correlations.

* 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

CombiChem/Excel Pro
Build combinatorial libraries in Microsoft Excel using reagents selected by ChemBioFinder.

* Windows Only

BioDraw Ultra
BioDraw Ultra makes drawing and annotating biological pathways quick and straightforward, adding an unmatched level of uniformity and detail. Drawing elements include membranes, DNA, enzymes, receptors, and reaction arrows, tRNA, Ribosomes, Helix Proteins, Golgi Bodies, G-Proteins, Immunoglobins, Mitochondrion and a Plasmid Map Tool. BioDraw Ultra now includes a biopolymer toolbar for drawing and editing peptide and nucleotide sequences using single and three letter codes, including beta and D-amino acids. The sequences can be expanded and contracted and sulfide and lactam bridges can be easily added.
ChemNMR Pro
ChemNMR can be used to accurately estimate 13C and 1H (proton) NMR chemical shifts. The molecule and the spectrum appear in a new window. The chemical shifts are displayed on the molecule and the spectrum is linked to the structure so that clicking on a peak in the spectrum highlights the related fragment on the molecule. With ChemNMR 13.0, the solvent can be specified as DMSO or CDCl3
Struct=Name Pro
Struct=Name contains the leading comprehensive methods for converting chemical structures into IUPAC chemical names and names to structures. It can be used for many types of compounds, including charged compounds and salts, bridged and fused ring systems, highly symmetric structures, isotopically labeled compounds and many other types of inorganic and organometallics.
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

MestRe Nova Std/Lite
MestRe Nova (MNova) Std is a 1D only application for data processing, visualization and analysis of NMR data. The program provides a variety of conversion facilities for most NMR spectrometer formats and includes the conventional processing, displaying and plotting capabilities of an NMR program, and more advanced processing techniques. MNova Std/Lite is a 1D only version of MNova which offers the user basic processing and analysis capabilities. The full version of MNova is available through the SciStore online store or directly through Mestrelab Research.
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

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

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

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

ChemBioDraw Ultra

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.

Control every aspect of arrows drawn, including arc, length, headstyle, dipole, no-go and more.

Draw biological pathways with common pathway elements such as membranes, DNA, enzymes, receptors, and reaction arrows. tRNA, Ribosomes, Helix Proteins, Golgi Bodies, G-Proteins, Immunoglobins, Mitochondrion and more!

Biopolymer Toolbar
Draw peptides and nucleotide (DNA, RNA) sequences using 1- and 3- letter codes. Includes natural L-, unnatural D- and beta amino acids. Simply switch between 1- and 3- letter codes and expand and contract labels. Insert linking and protecting groups with simple type-ahead functionality. Use the bond tool to create disulfide and lactam bridges, and cyclic peptides.

Draw both acyclic and snaking chains.

(W) See what structures look like in 3D in a floating window and open Chem3D with a single click from within ChemDraw.

Chemical File Format View demo clips of this feature
Reading & writing of chemical file formats including skc, mol v3000, sdf, spectra & reactions.

Mouse-over red box to read error description.

ChemNMR Solvent Selection
Users can now select whether they want the spectrum predicted in CDCl3 or DMSO.

ChemNMR User Proton Shift Database
Users can add their own shift correction data for proton prediction which can supplement the existing data used by the ChemNMR algorithm.

(W) Advanced property parameter including BP, MP and more.

CLogP/CMR provides the latest methodology for calculationg n-octanol/water partition coefficients and molar refractivity.

Custom Templates & Nicknames View demo clips of this feature

Search PerkinElmer Informatics databases for chemical structures in real time as you draw.

Expand Generic Structure View demo clips of this feature
Generate multiple structures from an "abbreviated" generic structure.

Floating Character Map View demo clips of this feature
Add special characters from any font instantly to any ChemDraw document.

Floating Periodic Table View demo clips of this feature
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.

High Color Documents and Templates View demo clips of this feature
Documents can contain over 16 million colors. Create high color pathway and element templates.

New compatibility mode allows ChemDraw to look and feel like your legacy drawing package.

ISIS-style Data SGroups
Data can be attached to objects.

Publication-quality EPS glassware art for use within your ChemDraw documents.

LogP
Calculate the logarithmic value of the n-octanol/water partition coefficient.

LogS
Calculate the logarithmic value of the aqueous solubility S of a compound. This value significantly affects its absorption and distribution characteristics.

Mass & Other Fragmentation Tools View demo clips of this feature
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.

Create multiple page documents and posters within a single ChemDraw file.

Name=Struct
Produce structures from systematic and common chemical structure names, and generate systematic IUPAC names from structures. Works for many types of compounds, including charged compounds and salts, isotopically labeled compounds, highly symmetric structures and many other types of organic, inorganic and organometallics.

Online Menu
(W) Draw a structure or model and immediately get online vendor information ChemACX.Com with the click of a button.

Paste Sequences
Paste sequences in FASTA format. Copy a text string describing a biopolymer as a series of single or multi letter residues, with valid separators (space, tab, dash), and paste it as a sequence with full chemistry.

pKa
Calculate the logarithmic value of the acid dissociation constant Ka, which is a quantitative measure of the strength of an acid in solution.

Create a plasmid map entering the number of base pairs in the plasmid map and specifying ranges for regions and locations and labels for markers.

Represent and manipulate polymers in ChemDraw.

Properties HotLink View demo clips of this feature
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 View demo clips of this feature
Allows specification of relationships between groups of stereocenters smaller than an entire molecule.

Rotation about Arbitrary Centers View demo clips of this feature
Change the center of rotation using adjustment handle on the Lasso and Marquee tools. Rotation will now be centered on the selected origin.

Save to Dropbox
Use Cloud storage via Dropbox to save, share and import ChemBio3D models in a secure but sharable Cloud location.

Draw peptide or nucleotide sequences using using 1 and 3 letter codes. The atoms are labeled with amino acid or nucleotide nicknames. The sequences can be expanded and contracted.

Identifies stereocenters using Cahn-Ingold Prelog rules.

Stoichiometry Grid View demo clips of this feature
Automatically track and update stoichiometry data for any user-defined chemical reaction.

Structure CleanUp
Improves poor drawings.

Structure Perspective Tool
Adjust the perspective of ChemDraw molecules with simple horizontal/vertical mouse movements.

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

(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.)

(W) Select multiple molecules and let Chem3D automatically align them with a target molecule.

(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.

(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.

(W) New conformational analysis tool allows the generation of MM2 energy plots.

(W) Chem3D uses openGL to provide high quality graphics display.

Formal Charges
(W) Assign Formal Charges to Atoms and Chem3D will generate delocalized charges automatically.

(W) GAMESS and Chem3D interface to GAMESS

Group Labels
(W) Display group labels in the Chem3D model view.

(W) Automatically display hydrogen bonds in the 3D view!

Kekule / Delocalized Display Mode
(W) Toggle between dashed line and alternating single-double bond representation of delocalized and aromatic bonds.

LogP
Calculate the logarithmic value of the n-octanol/water partition coefficient.

LogS
Calculate the logarithmic value of the aqueous solubility S of a compound. This value significantly affects its absorption and distribution characteristics.

(W) Built in support for MM2 to generate realistic 3D structures.

(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.

(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.

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

(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.

(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.

Spectrum Viewer
(W) Display spectral calculation results from 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 Ultra

3D Query/Finder
(W) Query ChemFinder database by 3D parameter.

ActiveX Control Boxes View demo clips of this feature
(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.

(W) The bio visualization add-on to ChemBioFinder allows you to create graphical representations of ChemBioFinder databases in order to identify trends and correlations within subsets of your data.

Chemical Searching View demo clips of this feature
(W) Search for (sub)structure, similarity, numeric values, text, chemical formula (including element ranges, element exclusions), date. Support for tautomers and alt groups.

Clustering Analysis
Discover similarities within sets of compounds and properties.

(W) Visually compare and rank structures based on values of selected properties and the cost profile associated with each property.

Hit List and Query Management View demo clips of this feature
(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.

(W) Merge hitlists with any logic: intersect, union, subtract, reverse subtract.

Multiple Data Views View demo clips of this feature
(W) View records one at a time, in a table view or a multiform view.

Plotting
(W) Plot one or two variables with a variety of plotting options. Hover over a point to view the corresponding chemical structure. Filter displayed points by any numeric variable using a slider control.

Plotting: Statistical Analysis and Customization
(W) Perform statistical analyses and display the results on the plot, modify the shape and color of plot points, add comment boxes, change axis label text and background color.

Plotting: Subform Plots
(W) Include miniature plots inside subform boxes for quick visualization of subform data on a per-compound basis.

Property Generation View demo clips of this feature
(W) Generate many types of physical property; populate database fields automatically or generate on-the-fly per record.

Python Scripting
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.

(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

(W) Generate a ChemDraw structure in MS Excel by typing in systematic chemical names for most substances.

BioDraw Ultra

Control every aspect of arrows drawn, including arc, length, headstyle, dipole, no-go and more.

Draw both acyclic and snaking chains.

Mouse-over red box to read error description.

Expand Generic Structure View demo clips of this feature
Generate multiple structures from an "abbreviated" generic structure.

Floating Character Map View demo clips of this feature
Add special characters from any font instantly to any ChemDraw document.

Floating Periodic Table View demo clips of this feature
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.

High Color Templates View demo clips of this feature
A set of high color pathway and element templates.

Mass & Other Fragmentation Tools View demo clips of this feature
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.

Create a plasmid map entering the number of base pairs in the plasmid map and specifying ranges for regions and locations and labels for markers.

Represent and manipulate polymers in ChemDraw.

Properties HotLink View demo clips of this feature
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 View demo clips of this feature
Allows specification of relationships between groups of stereocenters smaller than an entire molecule.

Draw peptide or nucleotide sequences using using 1 and 3 letter codes. The atoms are labeled with amino acid or nucleotide nicknames. The sequences can be expanded and contracted.

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.

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.

ChemNMR Pro

Predict Proton NMR spectra with splitting patterns. Also predict Carbon-13 NMR spectra. Spectra and peaks are linked to the structure for clear interpretation. Add your own shift correction data for proton prediction which can supplement the existing data used by the ChemNMR algorithm.

ChemNMR User Proton Shift Database
Users can add their own shift correction data for proton prediction which can supplement the existing data used by the ChemNMR algorithm.

Struct=Name Pro

Produce structures from systematic and common chemical structure names. It can be used for many types of compounds, including charged compounds and salts, highly symmetric structures and many other types of organic, inorganic and organometallics.

Produce names for many more types of compounds, including charged compounds and salts, highly symmetric structures, many types of inorganic and organometallic compounds, and others.

ChemScript Pro

Apply chemical business rules to chemical objects by using customizable scripts

MestRe Nova Std/Lite

Process and analyze 1D NMR FID (free induction decay) files.

Gaussian Interface

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