ChemBioOffice 2008

Daniel Oberlin

Director, Software Development

ChemBioOffice 2008The Desktop Productivity Suite for Scientists

ChemBioOffice

• The industry-standard desktop suite for chemists and biologists• Interoperates with and complements Microsoft Office• Integration with CambridgeSoft Enterprise Solutions• A vital productivity tool any organization

ChemBioOffice 2008The Desktop Productivity Suite for Scientists

ChemDraw Excellence

• Structure diagram generation– Rigorously conforms to the IUPAC conventions– Licensed commercially to other vendors

• Structure rendering– Highest quality – the details set us apart

• Name to Structure– More names, best accuracy– Error detection and correction

• Chemical data formats– More formats, best accuracy

• Ease of use– Most intuitive, most efficient

ChemDraw for Analysis

0123456PPM

(S)

H

HO

(R)

H

OHHOH

(R)(S)

(R)H

OOH

HO H

ChemBioDraw 11.0 New features and improvements

• New Chemistry Features– Sequence tool– Structure clean-up and stereochemistry enhancements– New reaction interpretation, SD file support, R-Group logic

• Improved productivity and application integration– Customizable themes and preferences – Hotlink to Databases, Chem3D Hotlink

• New drawing features– Flexible arrows– Freehand pen tool– Integrated BioDraw including new plasmid map

• 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 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 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 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

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

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

OR

HOHO

OHOH

OH

CHOR

S

OHH

R

HHO

R

OHH

CH2OH

OHH

(R)

OH

OH

ISIS/Draw compatibility mode in ChemDraw

Change ChemDraw, not your WorkflowCustomizable Themes and Preferences

ChemDraw

ISIS Compatibility

ISIS/Draw Compatibility Use ChemDraw in place of ISIS Draw

• ISISTM R-group Query Compatibility– Query a structure database using R-Groups and logical conditions

• SD File Support– Import an SD file with multiple structures into ChemDraw 11.0– ChemDraw will display all of 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

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

• A separate floating window shows a 3D model of the current structure– Chem3D must be also be installed

Chem3D Hotlink Integrated structural visualization

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 are opened in an external browser window so work in ChemDraw can continue…

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

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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/UXNNMRBruker 1D **

Aspect 2000/3000

Bruker 1D

Win-NMR Bruker 1D

JEOL GX/EX JEOL 1D

CDFF Nuts AcomNMR 1D **

JCAMP-DX 5.0 IUPAC 1D

NTNMr Tecmag 1DSwaN-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-to-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

Porphyrin s

Highest Presentation Quality Graphics 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

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

O

CH3

CH3H3C

SH SH

O

H3C

CH3H3C

SH SH

2,7,9-trimethyl-4aH -xanthene-4,5-dithiol

BioDraw Illustration of Biological and Biochemical Systems

cd 42

PAK

MEKK

SEK

JNK

MEK

ERK 1,2

ELK-1

AP-1 transcription factor

RAS

RAF CD3

Nucleus

ELK-1 Activatesc-fos transcription

Cytoplasm

Extracellular

Cytoplasm

SIGNAL 1

ANTIGEN PRESENTING CELL

c-Fos c-Jun

c-Fos c-Jun

Interlukin 2enhancer

BioDraw allows the illustration of…– Biological pathways– Cell macro-structures– Plasmid maps

… which may be combined with chemical structures, reactions, and other content from ChemDraw…

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) ImmunoglobinDNA 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

• BioDraw features are fully integrated into ChemBioDraw Ultra

Integrate Chemistry and Biology Drawings Facilitate Communication between Scientists

• Use any BioDraw tool in any ChemDraw document

• 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

ChemBio3D 11ChemBio3D 11

• Medicinal Chemists…–

Comparing structures and properties of trial compounds

–

Visualizing small molecules in a protein active site

–

Building new trial compounds

• Biochemists…–

Viewing and customizing the display of protein systems

–

Showing details of active site regions

Bio3D is for…

• All Chemists…

–

Easily generating realistic 3D structures using ChemDraw

–

Understanding molecular flexibility and motion using simulation

–

Creating high resolution images of chemical systems for publication

–

Embedding live, interactive models in web pages and PowerPoint

Chem3D is for…

Chem3D Bio3D

Both Come with ChemBio3D

ChemBio3DUltra

• Medicinal Chemistry Structure Browser–

Compare structures and properties

• MMFF94 Force Field Minimization–

More atom types and better parameters

• Improvements to the Model Explorer–

Drag-and-drop, improved performance

• And many other improvements…

ChemBio3D 11 New Features

Structure Browse

rNew for ChemBio3D 11

• Medicinal and cheminformatics groups 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 quickly using ChemDraw

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

Model Explorer Tree Control Efficiently explore the structure of large molecules

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…

• MMFF94 is equally applicable for proteins, small molecules, or systems containing both.

• The MMFF94 force field provides a richer set of atom types, so MMFF94 calculations may succeed in cases where MM2 calculations fail due to missing atom types.

MMFF94 Force Field Minimization Support for Protein Calculations

ChemFinder Chemical Database Management System

• View and Build Your Own Chemical Databases• Create your own forms• Store chemical structures, 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 ChemFinder

No 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

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

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

• 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

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)

New Workgroup solutions

• To date CambridgeSoft offered Desktop or Enterprise solutions. – Desktop solutions are adequate for individual users

– Enterprise solutions require Oracle and many days of services and customization. Fits large organizations.

• There was no offering for small groups that work collaboratively but do not have the resources to deploy a fully fledged enterprise solutions.

• New offerings:– ChemBioOffice Workgroup Ultra 2008

– ChemBioOffice Workgroup Pro 2008

ChemBioOffice: offering the right solution

ENotebook, Inventory & BioAssay Desktop

• SQL Server 2005 Express - self tuning RDBMS• Support multiple users• Supports Vista• 1-10 users• Database limit now doubled - 4GB

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

ENotebook, Inventory & BioAssay Workgroup

• Parallel Desktop and Workgroup products• SQL Server 2005• Easy upgrade from Desktop to Workgroup• No limit on the Database size• 10-100 users• Better performance, particularly with many users

• Basic features of ELN: • Audit Trails, AutoText, Stoichiometry Calculations,

Configurability, Document Pages, Extensive Data Types, Galactic spectra

• Share database - support multiple users• SQL Authentication• Uses ChemDraw 11

E-notebook Workgroup Eliminate hours writing & searching lab results

E-notebook Workgroup Eliminate hours writing & searching lab results

AutoText

Sections

ReactionConditions

StoichiometryGrid

CollectionTree

Reaction

Audit Trail

Inventory Workgroup Workgroup Chemical Inventory Management

• SQL Server Role-based Security• Cascading Location Model• Audit Trail - logs all changes relating to

Locations, Containers, and Substances• EHS, Reporting, Barcode Labels,• Suppliers/MSDS through integrated

ChemACX.com• Load your own MSDS, enter your own EHS

data, create reports with it.

• Utility to import Excel data• Structure intelligence using MolServer – can be

deployed on the DB server• Integration with ChemACX.Com• Reconcile Location Contents

Inventory Workgroup 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 Workgroup Storage and analysis for biological data

• Flexible Assay Definition model

• Multi-user access• Role level

permissions• Graphing

Enhancements• Report Engine

BioAssay, ENotebook & Inventory Workgroup Services Options

• On-site Support Services:• Migration Desktop Workgroup (SQL Server):

• 0-3 days of Support/Service Recommended

• Migration SQL Enterprise (Oracle):• Database schemas are similar; 3-15 days

• Installation/Configuration Services:• 1-3 Days On-site Assistance Recommended

• Training Services: • E-Notebook, Inventory, BioAssay Administrator, User Training Available • Training Courses are also available for ChemBioViz Desktop applications

BioAssay, ENotebook & Inventory Workgroup ASL

• Annual Site License

• 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)

• Site licenses reduce support load

• Multi-year site licenses reduce long-term cost

ChemBioOffice Annual Site License Cost Effective Collaboration

•

Unlimited usage within organization–

lower cost per user

•

All departments have access to the software

•

Updates and administrator support included

•

Software can be used on any machine–

lab, laptop, or home use

•

Site licenses reduce support load–

Individual online software download

•

Multi-year site licenses reduce long-term cost

•Thank you for your time!

Conclusion