Cam

bridgeSoft Solutions

ChemBioOffice 2008Overview

Mary-Ann MooreDirector, Global Marketing

ChemBioOffice 2008- The Desktop Productivity Toolkit for Scientists

ChemBioOffice

• Scientists Need Offices too!• ChemBioOffice is the

Desktop Standard for Research by Scientists

• ChemBioOffice provides the desktop tools scientists need, right at their fingertips

• ChemBioOffice integrates with Enterprise Solutions (such as the CambridgeSoft Enterprise and ELN suites) providing a Fully Integrated Scientific Management System that extends across the corporation

ChemBioOffice 2008 Applications- The Desktop Productivity Suite for Scientists

The ultimate chemistry & biology suite, designed to meet the needs of both chemists and biologists

• ChemBioDraw Ultra 11.0• MestReC Std • ChemScript Pro 11.0• ChemBio3D Ultra 11.0• ChemFinder Ultra 11.0 with support for Oracle• ChemBioViz Ultra 11.0 • BioAssay Ultra 11.0• Inventory Ultra 11.0 • E-Notebook Ultra 11.0• ChemDraw/Excel 11.0• CombiChem/Excel 11.0• ChemDraw and Chem3D ActiveX Pro Plugins & Controls 11.0• ChemINDEX (Index, RXN, NCI & AIDS)• 1-year subscriptions to ChemACX and ePub

ChemBioOffice Annual Site License-Cost Effective Collaboration

• Unlimited usage within institution (hence lower cost per user)

• All departments have access to the specific software they need

• Software updates and administrator support included

• Software can be used on any machine (lab, laptop, home use)

• Individual online software download means less administration

• Site licenses reduce support load

• Multi-year site licenses reduce long-term cost

Work faster with ChemDraw 11.0- You do more Chemistry

• Advanced Chemical Intelligence– Customizable Nicknames, Hot Keys, and Templates– Structure Clean-up Enhancements, New Reaction

Interpretation, SD file support , R-Group logic and more• Improved Productivity

– Customizable Themes and Preferences – LiveLink to Databases; Chem3D LiveLink– New Drawing Features continue to enhance communication

• Sequence Tools• Enhanced Arrows• New Freehand Pen Tool• Stereochemistry Enhancements

• Extended Platform Support: Windows Vista, MSOffice 2007, Native support of Intel on Mac

Work faster with ChemDraw- ChemDraw Reduces Drawing Time

Hotkey Result1 Change to single bond.

2 Change to double bond.

3 Change to triple bond.

4 Change to quadruple bond.

c Center a double bond.

l Position a double bond to the left.

f Bring a bond to the front.

a A

A or 5 Ac

b Br

Customizable Hotkeys

• Use Hotkeys to draw chemical structures in less than half the time

• Avoid going back to the Tools Palette to change tools - those mouse motions and clicks add up to a lot of extra time!

• Share Hotkey customizations with colleagues

Complex structures take seconds to draw vs.

minutes

• Save hours by using predefined rings, templates and drawings

• Create custom templates, reducing time for repeated experiments

Customizable Templates

Work faster with ChemDraw- ChemDraw Reduces Drawing Time

Reduce Document Clutter- Communicate key chemistry more effectively

Customizable Nicknames

• Simplify and speed up chemical drawings using Nicknames• Draw structures where parts of the molecule aren’t shown in full

detail, but instead are represented by a chemically intelligent labelthat can be expanded and contracted

• Define new nicknames in ChemDraw to fit your research

Reduce Document Clutter- Communicate key chemistry more effectively

Customizable Nicknames

• Simplify and speed up chemical drawings using Nicknames• Draw structures where parts of the molecule aren’t shown in full detail,

but instead are represented by a chemically intelligent label that can be expanded and contracted

• Define new nicknames in ChemDraw to fit your research

Reduce Document Clutter- Communicate key chemistry more effectively

Customizable Nicknames

• Simplify and speed up chemical drawings using Nicknames• Draw structures where parts of the molecule aren’t shown in full detail,

but instead are represented by a chemically intelligent label that can be expanded and contracted

• Define new nicknames in ChemDraw to fit your research

New Sequence tool- Easily Create Amino Acid, DNA, RNA sequences

• Draw peptide and nucleotide sequences

• Several modes:- Single-letter amino acid

tool- Three-letter amino acid

tool- DNA tool- RNA tool

• Termini are labeled depending on the type of sequence drawn

• Expand and contract single or multiple labels and sequences

NH2 COOHAla Cys Gly Thr

C

NH

O

HS

H

A

HN

O

G

HN

O

OH

T

NH

O

OH

Highest Presentation Quality Graphics- Instant Structure and Reaction Clean-up

H H

H

S

S S

S O

O

O

O

H O

O

OHH

• One click with Structure or Reaction Cleanup provides neater, more accurate drawings

• Compare to multiple undo’s and adjustments to the structure –significant time savings

• Fixed Lengths and Fixed Angles options• Major Improvements to algorithm in version 11 supports a wide

spectrum of structure types

Positioning of hashed and

wedged bonds

Selection of base ring in cyclic system

Vertically oriented

carbonylsRemoval of overlap: Bridged rings

Enhanced Reaction intelligence- Quickly identify reaction components

• New Command: Show Reaction Interpretation – helpful when illustrating complex mechanisms

• Allows users to re-arrange a reaction so that it is correctly interpreted

Enhanced Reaction intelligence- Quickly identify reaction components

• New Command: Show Reaction Interpretation – helpful when illustrating complex mechanisms

• Allows users to re-arrange a reaction so that it is correctly interpreted

• Color scheme– Reactant - red – Product - magenta – Above arrow - cyan – Below arrow - blue

Here is ChemDraw 11.0

Change ChemDraw, not your Workflow- Customizable Themes and Preferences

New in v11

Here is ISIS/Draw 2.5

Change ChemDraw, not your Workflow- Customizable Themes and Preferences

ISIS/Draw compatibility mode in ChemDraw

Change ChemDraw, not your Workflow- Customizable Themes and Preferences

New in v11

ISIS/Draw compatibility mode in ChemDraw

ChemDraw 11 Enhanced User Experience- ISIS Users get familiar interface plus ChemDraw benefits

New in v11

ISIS/Draw Compatibility- Use ChemDraw in place of ISIS Draw

ISISTM R-group Query Compatibility• R-Logic Queries: query a structure database using R-

Groups and logical conditionsNew

in v11SD File Support• New option to Import an SD file that contains data for multiple

structures into ChemDraw 11.0• ChemDraw will display all the structures in one drawing

Full MDL File Format Compatibility• Reading, writing of SKC, TGF, MOL, MOL V3000 & RXN files• Support for many other file formats for transfer of structures to

other applications and creating presentation quality graphics• Support for Data S-Groups – attach data to objects

New in v10

Full Compliment of Query features• Alternative groups, element lists, variable attachments and more

• “View 3D Preview” is a new menu item under the View menu

• A separate floating window shows a 3D model of the current structure as generated by Chem3D

• A current version of Chem3D must be installed

Chem3D LiveLink- Integrated structural visualization

New in v11

Database Gateway Livelink- Search structural databases in real time

• Real-time search– Search as you draw– Search all CS databases– Search internal databases

• Drill-down results– Click on data source name

to see results from that source

– Links open in external browser window so work in ChemDraw can continue

New in v11

Advanced Drawing Conventions - Stereochemistry enhancements

• ChemDraw 11 has been enhanced to recognize the common drawing styles that represent tetrahedral stereochemistry without using stereo bonds in their usual sense

• Changes are consistent with the latest IUPAC recommendations for the depiction of stereochemistry

• Examples:

SR

SOR

S

HO

HOOH

OHOH

S

R RR

ORHO

HO

OHOH

OH

CHOR

S

OHH

R

HHO

R

OHH

CH2OH

OHH

CS

F

F(R)

OH

OH

ChemDraw NMR Prediction– Helps confirm Chemical Structures

• 1H NMR includes splitting Patterns

• Calculate predicted 13C NMR spectrum

ChemDraw NMR Prediction– Helps confirm Chemical Structures

• 1H NMR includes splitting Patterns

• Calculate predicted 13C NMR spectrum

0123456PPM

MestReC Std processes 1D NMR Spectra- Chemists can analyze their results in seconds

Data Format Vendor Dimensions

VXR/Unity/Inova Varian 1D **

Gemini/VXR Varian 1D

XWIN-NMR/UXNNMR

Bruker 1D **

Aspect 2000/3000

Bruker 1D

Win-NMR Bruker 1D

JEOL GX/EX JEOL 1DCDFF Nuts AcomNMR 1D **

JCAMP-DX 5.0 IUPAC 1D

NTNMr Tecmag 1D

SwaN-MR Menarini 1D

SIEMENS NMR Siemens 1D

SIEMENS NMR Nicolet/GE 1D

BaselineCorrection

Phase Correction

Analysis

MestReC Lite Import File Formats

• Basic NMR processing and analysis - ideal for multiple chemists running large numbers of routine experiments

• Compliments ChemDraw’s NMR prediction capabilities** Full version of MestReC also reads 2D in this format

Isotopes

Inner salts

Lambda convention

Name = Struct now handles more structure types and has a typo recognition feature

Instantly Generate Structures from Names- Do more Lab work, less Drawing

HN

N

NH

N

porphyrin

Porphyrins

Highest Presentation Quality Graphics- Adjustable Shapes, Arrows and more

• Arrow Types include: No-go, unbalanced equilibrium, dipole, multiple arrowheads

• Adjustable Arrows – Full control over arrow properties including Curves, color fill and shading - illustrate complex chemistry/biology mechanisms

• Rotatable and adjustable geometric shapes – rectangles and ovals

• Color-faded geometric shapes –rectangles and ovals

Intuitive Freehand sketching tool

• The toolbar contains two items, “Draw Curve” (default) and “Edit Curve”

• Holding the “Shift” key reduces the amount of smoothness• The curves created can be further modified by selecting

and dragging control points

New in v11

• BioDraw features are fully integrated into ChemBioDraw Ultra

• Use any BioDraw tool in any ChemDraw document

• Excellent collaborative tool

Integrate Chemistry and Biology Drawings- Facilitate Communication between Scientists

Integrate Chemistry and Biology Drawings- Facilitate Communication between Scientists

One or Two-substrate enzyme Receptor Ion Channel Helix Protein Linear membrane Arc membrane Golgi body Cloud G-Protein (alpha, beta or gamma subunit) Immunoglobin DNA Micelle Ellipse membrane Endoplasmic Reticulum Mitochondrion

Draw Biological Pathways

BioDraw New Drawing tools- Enhanced illustration of biological processes

• New tRNA Tool• New Ribosome Tool• New Plasmid Maps• DNA helix strands can

now be selected individually for modification

• Protein helix strands and cylinders can now be individually selected and modified

• The Annotation tool allows the user to add information to objects. The information will be stored and show as a keyword and content

– Keyword: will describe the type of information– Content: will contain the information.

• A list of keywords has been pre-defined (Description, Name, Other Info, and Type)

• The user also has the option to add new keywords

Annotations- Add information to Objects in ChemBioDraw

• Medicinal and cheminformaticsgroups can access high quality, easy to use visualization and computation tools at a low cost

• Visualize results from Computational Chemistry Group - assist in designing the next round of synthetic targets

• Protein and Nucleic Acid Ribbon Diagrams provide insight into tertiary and quaternary structure of proteins and protein complexes

Quality visualization on the Desktop- Structural insights, Team collaboration

ChemBio3D Ultra

ChemBio3D Ultra: ChemDraw Panel- Build models in a fraction of the time

Improved in v11

• Easily draw 3D structures using embedded ChemDraw window• Always in-sync with 3D view• All the time saving benefits of ChemDraw available within Chem3D!

Model Explorer Tree Control- Efficiently explore the structure of large molecules

Improved in v11

Medicinal Chemistry Structure Browser- Quickly compare small molecules and properties

• The Structure Browser allows users to easily “flip through” a collection of small molecules and compare their structures and properties

Chem3D Visualization- More Visualization and Display Options

Kekule / Delocalized Display Mode• Toggle between dashed line and

alternating single-double bond representation of delocalized and aromatic bonds.

Atom Properties• New Atom Property Table in v11• Color-code your model based on

virtually any property• Partial Charges from QM

Calculations and Force field atom types and charges treated as atom properties

• Specifically designed to perform energy calculations and minimizations on proteins and other biological structures

• More Atom types and better parameters

• MMFF94 was parameterized as a combined organic/protein force field, and so is equally applicable for proteins, small molecules, or systems containing both. Additionally, the MMFF94 force field provides a richer set of atom types than MM2, so MMFF94 calculations may succeed in cases where MM2 calculations fail due to missing atom types

MMFF94 Force Field Minimization- Support for Protein Calculations

• Import SD files, containing multiple structures - two, three, or even dozens and view using the new Structure Browser

• Using the Structure Browser, browse through the list of structures and view each one in the Model window.

• Chem & Bio 3D 11.0 now supports the Schrödinger Maestro file format for importing and exporting molecular models

New File Formats- SD Files and Support for Maestro Format

Live Models in PPT - Collaboration and Communication

• Embed Chem3D models in PowerPoint file• Rotate and zoom Chem3D models while giving a

presentation!

« Chem3D Embed »

ChemBio3D Extensions and API- Gaussian and Jaguar Interfaces

Gaussian• Predict NMR, IR and Raman spectra • Support multi-step jobs and partial optimizations • New DFT tab • Monitor Gaussian Link processes

Jaguar• Surfaces: Total Charge Density surface, Total Spin Density

surface, Molecular Electrostatic Potential surface and Molecular Orbital surface

ChemFinder - Chemical Database Management System

• View and Build Your Own Chemical Databases• Create your own forms• Store chemical structures, physical properties, notes and tables of

data• Integrated with ChemDraw• Search data by

– Chemical structure (including sub-structure)– Wild card text searches– Numeric range searches

ChemFinder - Chemical Database Management System

Main toolbarTitle bar

Form

Text toolbar

Search toolbar

Structure

Shortcutmenu

box

toolbar

Mainmenu

Recordtoolbar

Datatable

Statusbar

Mainform

Frameddata box

Subform

Tableheader

Totaldatabase size

Currentlist size

Currentrecord

Queryindicator

Addindicator

Read-onlyindicator

BioViz

Data visualization and analysis right in ChemFinderNo need to switch back and forth to other apps

Analyses are saved with the form

Get more out of your data- Analysis right in ChemFinder with BioViz

Improved in v11

BioViz

Data visualizationPlot any numeric values

Flexible plot styles and display

Filter plot by any numeric criteria

Color plots by hitlist

Synchronization between plots

Data analysisStatistics, regressions

List manipulation

Mouse over points to show details

Get more out of your data- Lots of options with BioViz

Improved in v11

Get more out of your data-Chemically Intelligent Plots

• Integrated with BioViz

• Sortable by R-group

• Plot according to substituent membership

R-Group tables and R-Group analysis

Get more out of your data-Subform data at a glance

Subform plots• You can create a variety of subforms with ChemFinder including

miniature plots insidesubform boxes which plot one or two columns of numeric data from the set of records showing in the subform.

Compound Profiles- Compare structures based on Properties

Compound profilesVisually compare and rank structures based on values of selected properties and the cost profile associated with each property.

• Programming with Python- Python scripts can be attached to form buttons or trigger events,

can be developed and debugged in the enhanced Script Editor --now featuring interactive line-by-line execution -- and output can be displayed in a new dockable text window

• Integrated with ChemScript

ChemFinder 11 Programming Options- Python, ChemScript and CAL

ChemFinder/Office- Find molecules of interest on your computer

• Little known but extremely useful utility in ChemBioOffice Ultra• Search drives, desktop, or network for structures, reactions

• All search types: sub-, full-structure, similarity, formula, molweight

• Search databases, structure files, MS Office documents

• Double-click calls up original source• Refine and export hit list to any

destination

• Add chemical structures and other data from ChemDraw, MDL SDFiles or a ChemFinder database to an Excel spreadsheet

• Convert Names or SMILES Strings to Structures• Search using the same search features as

ChemFinder• Perform calculations on chemical structures

Chemical Intelligence within Excel- Chemical calculations on Multiple Structures

ChemDraw/ExcelISSTRUCTUREISREACTIONCHEM.FORMULACHEM.MOLWEIGHTCHEM.NUM.HBAACCEPTORSCHEM.NUM.HBDONORSCHEM.SMILESCHEM.COMPOSITIONCHEM.NUM.ATOMS

Property FunctionLogP CHEMPROP.LOGPMolar Refractivity CHEMPROP.MRHenry’s Law Constant CHEMPROP.HENRY.LAW.CONSTANTBoiling Point CHEMPROP.BOILINGFreezing Temperature CHEMPROP.FREEZINGCritical Temperature CHEMPROP.CRITICAL.TEMPCritical Pressure CHEMPROP.CRITICAL.PRESSURECritical Volume CHEMPROP.CRITICAL.VOLUMEHeat of Formation CHEMPROP.HOFGibbs Free Energy CHEMROP.GIBBSIdeal Gas Thermal Capacity CHEMPROP.IDEAL.GAStPSA CHEMPROP.TPSA

Improved in v11

Combinatorial Chemistry within Excel- Automatic Generation of Product Lists

CombiChem/Excel• Enter a reaction with generic reactants & products with R-groups and

reagents reagent lists

• CombiChem/Excel generates the resulting product list – no need to draw the resulting structures by hand

• Use Excel and ChemDraw/Excel tools to generate properties for the products and manipulate the data, such as re-ordering of products based on properties such as molecular weight

• Prior Limits on the number of products lifted in newer versions, with option to enumerate into a ChemFinder database (no limit)

BioAssay, ENotebook & Inventory- Multi-user access with SQL Server 2005

• SQL Server 2005 Express - self tuning RDBMS• Support multiple users• Database limit now doubled - 4GB

For example: Inventory with 1000 compds + 1000 containers + 1000 MSDS 0.1 MB pdfs = 140 MB

• Supports Vista

http://scistore.cambridgesoft.com/software/product.cfm?pid=84http://scistore.cambridgesoft.com/software/product.cfm?pid=5044

Inventory Ultra - Desktop Chemical Inventory Management

• SQL Server Role-based Security

• Cascading Location Model• Audit Trail - logs all changes

relating to Locations, Containers, and Substances

• Structure intelligence using MolServer – can be deployed on the DB server

• Utility to import Excel data• Integration with ChemACX.Com• Reconcile Location Contents

Inventory Ultra - Desktop Chemical Inventory Management

• Save money: know which chemicals you have, and where they are

• Produce customized reports

– OSHA compliance– Controlled

substances– Out of Date Stock– EHS Reporting– Barcode Labels

BioAssay 11- Storage and analysis for biological data

• Flexible Assay Definition model

• Multi-user access• Role level

permissions• Graphing

Enhancements• Report Engine

http://scistore.cambridgesoft.com/software/product.cfm?pid=84

E-notebook Ultra Desktop- Eliminate hours writing & searching lab results

AutoText

Sections

ReactionConditions

StoichiometryGrid

CollectionTree

Reaction

Audit Trail

• Supports multiple users

• SQL / Windows Authentication

• Uses ChemDraw 11

ChemScript Pro and Ultra- Chemical Scripting Language

• Based on over 20 years of development from the people who brought you ChemDraw

• Allows manipulation of 2D & 3D chemical structures • Access to a wide range of property calculations • Wide range of chemical structures available (Substructure,

Similarity, Maximum Common Substructure) • Clean and Align structures • Apply business rules (nitro group transformation, tautomeric

forms) • Accessible through popular, robust development environments

(Python, .Net etc) • Salt stripping functionality with customisable salt table • Supports wide variety of file formats (CDXML, SD, Mol,

SMILES, INCHI)

Powerful scripting language for the Searching, Manipulation and calculation of Chemical Structures

Cam

bridgeSoft Solutions

ChemBioOfficeOverview

Mary-Ann MooreDirector, Global Marketing

Slide Number 1Slide Number 2ChemBioOffice 2008 Applications� - The Desktop Productivity Suite for ScientistsChemBioOffice Annual Site License�-Cost Effective CollaborationWork faster with ChemDraw 11.0�- You do more ChemistryWork faster with ChemDraw�- ChemDraw Reduces Drawing TimeWork faster with ChemDraw�- ChemDraw Reduces Drawing TimeReduce Document Clutter�- Communicate key chemistry more effectivelyReduce Document Clutter�- Communicate key chemistry more effectivelyReduce Document Clutter�- Communicate key chemistry more effectivelyNew Sequence tool�- Easily Create Amino Acid, DNA, RNA sequencesHighest Presentation Quality Graphics�- Instant Structure and Reaction Clean-upEnhanced Reaction intelligence�- Quickly identify reaction componentsEnhanced Reaction intelligence�- Quickly identify reaction componentsSlide Number 15Slide Number 16Slide Number 17Slide Number 18ISIS/Draw Compatibility �- Use ChemDraw in place of ISIS DrawChem3D LiveLink� - Integrated structural visualizationDatabase Gateway Livelink�- Search structural databases in real timeAdvanced Drawing Conventions �- Stereochemistry enhancementsChemDraw NMR Prediction�– Helps confirm Chemical StructuresChemDraw NMR Prediction�– Helps confirm Chemical StructuresMestReC Std processes 1D NMR Spectra�- Chemists can analyze their results in seconds�Slide Number 26Highest Presentation Quality Graphics�- Adjustable Shapes, Arrows and moreIntuitive Freehand sketching toolSlide Number 29Integrate Chemistry and Biology Drawings�- Facilitate Communication between ScientistsBioDraw New Drawing tools�- Enhanced illustration of biological processesAnnotations�- Add information to Objects in ChemBioDrawSlide Number 33ChemBio3D Ultra: ChemDraw Panel�- Build models in a fraction of the timeSlide Number 35Medicinal Chemistry Structure Browser�- Quickly compare small molecules and propertiesChem3D Visualization�- More Visualization and Display OptionsMMFF94 Force Field Minimization�- Support for Protein CalculationsNew File Formats�- SD Files and Support for Maestro FormatLive Models in PPT �- Collaboration and CommunicationChemBio3D Extensions and API�- Gaussian and Jaguar Interfaces�ChemFinder �- Chemical Database Management SystemSlide Number 43Get more out of your data�- Analysis right in ChemFinder with BioVizGet more out of your data�- Lots of options with BioVizGet more out of your data�-Chemically Intelligent PlotsGet more out of your data�-Subform data at a glanceCompound Profiles�- Compare structures based on PropertiesSlide Number 49ChemFinder/Office�- Find molecules of interest on your computerChemical Intelligence within Excel�- Chemical calculations on Multiple StructuresCombinatorial Chemistry within Excel�- Automatic Generation of Product ListsBioAssay, ENotebook & Inventory�- Multi-user access with SQL Server 2005Inventory Ultra �- Desktop Chemical Inventory ManagementInventory Ultra �- Desktop Chemical Inventory ManagementBioAssay 11�- Storage and analysis for biological data Slide Number 57ChemScript Pro and Ultra�- Chemical Scripting LanguageSlide Number 59