Chem3D Users Manual - CambridgeSoft

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DISCOVERY • Reagent lists can be drawn from varied sources • Reaction based library generation allows for evaluation by product or reagent • Data management is simplified and library specifications are available to others on the network Finding Reagents Flexibility is the key when dealing with databases of chemical compounds. CombiChem Enterprise can use reagent lists from a variety of different sources: SD files, ChemFinder databases, ChemFinder hit lists, ChemOffice WebServer hit lists, ChemACX Database, or directly from the user via ChemDraw. Regardless of the source, CombiChem Enterprise produces a list of reagents which match a particular generic reactant. The chemist then chooses which of the compounds to use for generating products. Getting Results Once the chemist has given CombiChem Enterprise a set of reagents for each of the generic reactants in the reaction scheme, the software generates the set of products which would result from running the experiment. CombiChem Enterprise evaluates the products using several in silico methods, and the chemist can then choose which compounds to keep and which ones to reject. After the products have been generated, the software provides product information for each of the reagents. The chemist can use that information, for example, to trim away reagents having few or no products which pass the Lipinski Rule of Five test. Finally, the products are laid out on plates based on user-definable plate layouts. Integration with E-Notebook Keeping track of compound library data can be a challenge: which reagents led to this product, which product goes with that spectrum, what was in the mixture used in this thin layer chromatography CombiChem Enterprise provides ways to organize the data and navigation is simple. When used with E-Notebook Enterprise, the data for a library of shared compounds, and the entire experiment, is automatically documented and made available to the entire organization. EMAIL info@cambridgesoft.com WWW www.cambridgesoft.com TEL 1 800 315–7300 INT’L 1 617 588–9300 FAX 1 617 588–9390 MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge, MA 02140 USA ChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft ©2002. All other trademarks are the property of their respective holders. All specifications subject to change without notice.
RESEARCH & BioAssay HTS Biological Assay and High Throughput Screening BioAssay HTS BioAssay HTS provides scientists with an effective way of managing test results for biological and other kinds of experiments intended to assess the efficacy of compounds. Suitable for both plate-based high throughput screening assays and smaller-scale lead optimization experiments, BioAssay HTS provides researchers with simple tools for setting up their models in a database, uploading data, automating calculations and reporting on their findings. User Friendly Assay Management Even for the most basic protein assays, the independent and dependent variables used by the biologist to quantify efficacy can vary substantially from assay to assay. The underlying requirement that follows from this variability is for a flexible data management system that can adapt quickly to different assays and biological models. With BioAssay HTS, researchers or IT support staff simply define the observables and calculations that make up the assay. The database does the rest. Users can set up unlimited levels of drill-down. This allows users, for example, to click an IC50 and see a graph of percent inhibition versus concentration. Click again, and the software displays the original triplicate results, with outliers marked. The software even supports complex in vivo models. Automated Curve Fitting & Data Analysis Flexible Assay Definition Tools
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ChemOffice.Com ® ChemOffice ® Che
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License Information ChemOffice, Che
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· Licensed users of ChemOffice Ent
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computer, except as provided below.
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Q: IS IT OK TO COPY MY COLLEAGUE’
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A Guide to CambridgeSoft Manuals An
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Administrator Setting Molecular Sur
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Administrator Methods Available in
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Administrator Defining Atom Types.
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Administrator • CambridgeSoft
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Administrator The Calculation Toolb
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Administrator atoms are relatively
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Administrator • From the Computat
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Administrator The following table d
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Administrator When Correct Atom Typ
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Administrator 3. Type the atom type
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Administrator New in Chem3D version
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Administrator 3. Hold down the Shif
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To position a plane in your model p
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Administrator For example, consider
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Administrator If you want to displa
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Administrator Example: To examine t
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Administrator Chem3D provides two o
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Method Type Advantages Disadvantage
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Administrator activation barriers.
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Administrator The Compute Propertie
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Administrator TRIPLET QUARTET QUINT
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Administrator criteria, to optimize
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Administrator Molecular Surfaces Mo
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Administrator 3. Click in the model
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Keyword Description 7. On the Prope
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Administrator Hyperfine Coupling Co
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Administrator 198•MOPAC Computati
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Property Description Property Descr
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Property Description Error Message
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Administrator COMPND ATOM HETATM CO
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Parameter Table Use Parameter Table
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Administrator Adding Parameters to
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