ChemBioFinder for Office 13.0
Contents
1. Struct C Program Files Ca J 1 53 Taxol mol C Program Files Ca 10 480 1 1 Stucti 2 benzene cdx C Program Files Ca 788 1 1 Stuch i benzview cdx C Program Files Ca 776 1 1 Struct S test cdx C Program Files Ca 3846 1 1 Struct Sh test2 cdx C Program Files Ca 2 350 1 1 Stuct sy lt gt Ready 7 Use the previous and next arrows on the Record Search toolbar to navigate through the hits If ChemBioFinder for Office 13 0 finds no hits a warning message appears To refine your search so that Chem BioFinder has a greater possibility of finding hits use the Search Options tab Searching by multiple properties You can search for a chemical structure chemical formula molecular weight or any combination of these properties simultaneously To do so 1 Click New Search 2 Do the following To search for a specific molecular weight type a molecular weight g in the Mol Wt text box To search for a molecular weight within a range type a range of molecular weights g with lt or gt in the Mol Wt text box Tosearch for a chemical formula type a chemical formula in the Formula text box To search for more than one criterion structure formula or molecular weight specify the appropriate criteria in the respective fields Chapter 1 ChemBioFinder for Office 13 0 4 of 19 Da PerkinElmer For the Better ChemBioFinder for Office 13 0 _ Note When you search by chemical structure2. formula and molecular weight ChemBioFinder for Office 13 0 uses all the criteria together 3 Click Find Now a ChemBioFinder for Office 13 0 shows all of the files with the properties that you specify in the hit list window b If ChemBioFinder for Office 13 0 finds no hits a warning message appears c To refine your search so that ChemBioFinder has a greater possibility of finding hits use the Search Options tab To expand your search use the Look In tab For more information see Refining your search on page 8 Browsing search results You can view the search results in the hit list The hit list displays all of the files in which your search found matching structures Name In Folder File Size Total Hits Type A 98 Ibuprofen cdx C Program Files4Ca 1 055 1 1 Struct E23 Taxol mol C Program Files Ca 10 480 1 1 Struct S benzene cdx C Program Files Ca 788 1 1 Struct S benzview cdx C Program Files4Ca 776 1 1 Struct S test1 cdx C Program Files4Ca 3 846 1 1 Struct S test2 cdx C Program Files4Ca 2 350 1 1 Struct ay Si kinig IS Ready rec 1 list 7 db 7 Figure 1 2 A ChemBioFinder for Office 13 0 hit list To view the search results To view the entire Hit List use the scroll bars Todisplay each hit in a given file in the Structure window select the file in the Hit List and use the arrows in the Search Record toolbar Id 4 48 D gt Dl a To disp
3. results in ChemBioFinder 1 Open ChemBioFinder 13 0 2 Go to File gt Import gt Structures 3 Select the database from the Open Chemical Structures dialog box Chapter 2 CombiChem 16 of 19 ChemBioFinder for Office 13 0 PerkinElmer For the Better Index A ActiveX control 12 B browsing search results 5 C ChemDraw ActiveX control 12 ChemPFinder Office customizing 10 preferences 11 search options tab 9 send to menu 7 settings 10 Ul 1 CombiChem 13 D data source find chemical structures window 1 E entering a template 13 enumeration 14 exporting to another application 7 F files DSD 6 Index 17 of 19 ChemBioFinder for Office 13 0 I F PerkinEl For the Better SDF selecting with look in tab selecting with open file menu gt N WO Q formula searching by molecular weight searching by 4 preferences in ChemFinder Office 11 reaction template basics 13 refining your search overview 8 refining your search search tools 10 saving data sources directory paths to search files search results a O O OQ Q search results searching by chemical formula by chemical structure by molecular weight by multiple properties ao A A O A by selected files Index 18 of 19 ChemBioFinder for Office 13 0 directory paths DSD files enter query refining restore previous query save results search tools sending to another application templates entering working with reaction templ
4. the shortcut key to be removed from the Current Keys list oa A WN Click Remove and the click Close to exit the Customize window Changing preferences To change the ChemBioFinder for Office 13 0 preferences 1 Goto File gt Preferences The Preferences window appears 2 Take the appropriate action type the path in the Startup directory text box or choose a directory for the Look In tab to j click to browse to a directory Chapter 1 ChemBioFinder for Office 13 0 110f19 Ba PerkinElmer For the Better ChemBioFinder for Office 13 0 open to at startup This setting does not affect query properties type the number or click the up and down arrows specify the number of most recently open in the Number of recently used files to files to show in the File menu show on File menu box to set a whole number between 0 and 20 open the last file you used when you wae click Reopen last source on startup launch ChemBioFinder for Office 13 0 show all files in the directory tree in the click Show files in directory tree Look In tab use the ChemBioDraw ActiveX control to click the ChemBioDraw style button draw and edit structures open ChemBioDraw to draw and edit f ee click ChemBioFinder style radio button structures 3 Click OK Chapter 1 ChemBioFinder for Office 13 0 12 of 19 ChemBioFinder for Office 13 0 I PerkinElmer For the Better CombiChem Using the CombiChem engin
5. 0 Ul appears as shown below Chapter 1 ChemBioFinder for Office 13 0 1 of 19 Ba PerkinElmer For the Better ChemBioFinder for Office 13 0 Export hits Find Chemical Structures ile Edit View Record Search SendTo Help d 1E gt 0 E Structure Look In Search Options Find Now Substructure Full Structure C Similarity Formula Mol Wt Identity E ee Figure 1 1 The ChemBioFinder for Office 13 0 user interface A main menu B standard toolbar C structure win dow D formula text search box E record counter F structure search type options G show hide list H search rec ord toolbar 1 molecular weight search box Selecting files to search You can search for files that are stored locally or on a network You can browse through these types of sources a Microsoft Word documents Microsoft Excel spreadsheets a Microsoft PowerPoint files a ChemBioFinder databases a ChemBioDraw files a SD Files a SIS Draw files Selecting files from the File menu You can search for a structure in a specific file or data source To do so 1 Go to File gt Open The Open dialog box appears 2 To select a file or a data source to search do one of the following Inthe File Name text box type the name of the file to search Chapter 1 ChemBioFinder for Office 13 0 2 of 19 ChemBioFinder for Office 13 0 I p PerkinElime For the Better a Use the directory tree in the Open
6. Chemical Structures window to browse to a file 3 Click Open When you open a single file the first structure in the file appears in the Structure window You can browse through the file using the previous and next arrows in the Search Record toolbar Selecting files with the Look In tab Use the Look In tab to search for a structure in multiple files The Look In tab shows all the data sources on your mapped network CD ROM floppy and hard drives You can select entire folders to search or multiple individual files using the checkboxes next to the file names To look for a structure in specific files or data sources 1 Click the Look In tab The files and data sources appear in a tree directory _ Note You can set Preferences to keep the file names hidden in the directory tree For more information see Chang ing preferences on page 11 2 Select the file type from the Files of type drop domn list 3 Select the check box next to the file s or data source s to be searched 4 After selecting the data sources click the Structure tab to retum to the Structure window Searching by chemical structure You can find chemicals based on their structure You can perform either a substructure full structure similarity or identity search 7 Note Any search method that you use in ChemBioFinder can also be used in ChemBioFinder for Office 13 0 To search by chemical structure only 1 Do one of the following From the Look In t
7. HUMAN HEALTH ENVIRONMENTAL HEALTH ChemBioFinder for Office 13 0 User Guide Pa PerkinElmer For the Better ChemBioFinder for Office 13 0 gt PerkinElmer For the Better Table of Contents Chapter 1 ChemBioFinder for Office 13 0 2 22 22 2 2 occ coe nce 00000000 anaro 22222222 1 The user interface Ul 0c cc ccc ccc ccc cece ce eee eee eee eben ee eee beeen eee e eee raaraa narrar rannen 1 Selecting files tosearch eee 2 Searching by chemical structure 3 Searching by multiple properties eee cc cece cece cece cece cece cece cece cece ecceeeeeeeeeeeees 4 Browsing search results 0 0 22 2 c cece cece cece cece eee e ccc ce cee cecceeeceeeeeeeeeeeeeeeeeeees 5 Saving files or datasources a 6 Searching DSD files e eee e eee e cece cece cecccccccseeeeeeees 6 Sending a file to another application eee eee ee eee cece cece cece ccc aaeain aarnior 7 Refining your search 2 2 e daaa Aaaa cece cece cece cece E EADAE oE araara nana 8 Changing the interface appearance 2 2 eee 10 Chapter 2 CombiChem 2 2 2 0 2 2 2 0 c cece ec c ccc eee e cece cece eee e cece cece cece eeeceeececeeeeeeeeesesees 13 Working with reaction templates 0 2 e cece eee c ec ee aa aa eccceeececeeeeeees 13 Entering a template o occ e cece eee e cence cece e eee eeecenseeeesesseseeeeenes 13 APA 17 Tabl
8. Now Search Options Select from the options described below to modify your search the tetrahedral stereochemistry of the target structure to match Match tetrahedral stereo that of the query structure the double bond stereochemistry of the target structure to match Match double bond stereo that of the query structure to allow fragments in the query to overlap share one or more f Fragments may overlap atoms in the target any reaction center present in the query to overlap with reaction centers in the target This preference applies only to reaction Hit must overlap reaction center searching to allow hits to contain molecular fragments in addition to that Haha i Extra fragments may be present in hit which was hit by the query to allow uncharged carbon atoms in the query to match charged carbon atoms in the target Charged atoms in the query must I Match any charge on carbon always match charged atoms in the target regardless of this set ting to allow uncharged atoms in the query to match charged atoms in the target Charged atoms in the query must always match Match any charge on heteroatom charged atoms in the target regardless of this setting to allow a query drawn as absolute hash wedge bonds to hit a I j Absolute center hits relative target stored as relative to match a relative relationship between tetrahedral ster Relative tetrahedral stereo eocenters ChemBioFinder for Office 13 0 dis
9. ab select files to search a Goto File gt Open or choose a file from the most recently used list of files For more information about opening files to search through see Searching DSD files on page 6 Click New Search Click Edit Structure Double click in the structure window The ChemBioDraw plug in tools palette appears a A O N Draw the query structure in the Structure window using appropriate ChemBioDraw tools You can also copy a structure from ChemBioDraw or from ChemBioFinder database and paste it in the Structure window For more information about using the ChemBioDraw tools see the ChemBioDraw User Guide 6 Click Find Now g Note If the Find Now button is grayed out you have not selected a file or directory to search Click the Look In tab and make a selection Chapter 1 ChemBioFinder for Office 13 0 3 of 19 Ba PerkinElmer For the Better ChemBioFinder for Office 13 0 ChemBioFinder for Office 13 0 shows all the files containing the query structure in the hit list window as shown below Each entry in the hit list is a data source which may contain multiple hits Find Chemical Structures DER File Edit View Record Search SengTo Help gt ted e 4 4 fH gt NO 9 Structure Look In Search Options 9 amp so New Search HO No AM Substructure Full Structure C Similai ity Mol Wt C Identity Formula cisH1e020 206 285 f a lt lt
10. ates Index pP PerkinElmer For the Better 10 10 10 13 13 19 of 19
11. ction 1 In ChemBioFinder for Office 13 0 click Edit Structure Depending on your Preferences settings this will either open ChemBioDraw or activate the ChemBioDraw ActiveX control 2 Draw a generic reaction For more information on generic structures see the ChemBioDraw Users Manual Using a ChemBioFinder 13 0 database You can create a database of generic reactions in ChemBioFinder 13 0 ChemBioFinder for Office 13 0 can open CFX files directly and browse through them Once you have a generic reaction in the Structure window do the following 1 Go to Search gt Enumerate The Combi Enumerator window appears showing the reaction you drew in the Structure window To add another step to the reaction click Add Step You may then edit the reaction in ChemBioDraw by double clicking in the window or continue with the current reaction Combi Enumerator Reaction Analysis HO 2 O O H20 A N Enter or edit the generic reaction to be enumerated then click the Analysis tab Add Step Cancel Figure 2 2 Adding a step 2 Click the Analysis tab An analysis of the reaction steps appears below the reaction display Chapter 2 CombiChem 14 of 19 ChemBioFinder for Office 13 0 PerkinElmer For the Better Combi Enumerator Reaction Analysis Reactant A Overall reaction A B gt C D2E Step 1 A B gt C D Step 2 C D gt E Generic reactants A If analysis succeeds click Reacta
12. e of Contents ChemBioFinder for Office 13 0 I o PerkinElmer For the Better ChemBioFinder for Office 13 0 ChemBioFinder for Office 13 0 lets you search for chemical structures in data sources such as documents and data bases It is installed when you install ChemBioOffice Ultra You can browse through these types of sources Microsoft Word documents Microsoft Excel spreadsheets a Microsoft PowerPoint files ChemBioFinder databases a ChemBioDraw files SD files a SIS Draw files You can search files by a chemical structure chemical formula a molecular weight You can also run structure searches using the ChemBioDraw plug in with the following options substructure a full structure a similarity identity You can save frequently used collections of data sources documents and databases in Data Source Definition DSD files This enables you to have ChemBioFinder for Office 13 0 search through one DSD file instead of search ing through multiple data sources one at a time Using CombiChem with ChemBioFinder you can also generate generic reaction queries to be used in searching For more information see CombiChem on page 13 You can perform queries view search results and save results to a file to view later or send the hit list to other appli cations such as Microsoft Word Microsoft Excel ChemBioFinder ChemBioDraw and ChemACX com search The user interface Ul The ChemBioFinder for Office 13
13. e with ChemBioFinder for Office 13 0 lets you generate virtual libraries for combinatorial experiments These libraries can be drawn from any type of file that ChemBioFinder for Office 13 0 can read and are stored in MST format databases Working with reaction templates First you enter a reaction template with R groups at the variable sites in your base structures and then search for reactants based on these structures CombiChem puts the final product structures together and creates a virtual library For more information on R groups see the ChemBioDraw 13 0 user guide Reaction template basics Here s is an example of a reaction template that CombiChem supports R2 R2 Ry Ry HO NH3 N N H O N H R2 Ry NH Figure 2 1 A reaction template A reaction template must meet these specifications a All sites of variability require unique R group designations Solvents catalysts and other real world elements should not be included in the reaction template drawing Multi step reaction templates are supported Entering a template There are two ways to enter a CombiChem template in ChemBioFinder for Office 13 0 a Create a generic reaction in ChemBioDraw or with the ChemBioDraw ActiveX control Chapter 2 CombiChem 13 of 19 ChemBioFinder for Office 13 0 7 PerkinElmer For the Better a Create a ChemBioFinder 13 0 database of generic reactions ChemBioDraw and ChemBioDraw ActiveX To draw a generic rea
14. lay the actual file double click on a file name in the Hit List or right click and select Activate with any of these extensions a doc a xls a cdx a cfx The application in which the structure was saved opens In Microsoft Word the application opens to the first hit in the document You can also use the hit list context menu to add or remove hit list records To add or remove hit list records 1 Ina Hit List with records right click a record 2 Select Add from the context menu The Open Chemical Structures window appears 3 Double click the file to add to the Hit List or type the name of the file in the File Name text box Chapter 1 ChemBioFinder for Office 13 0 5 of 19 ChemBioFinder for Office 13 0 I i AN PerkinElime For the Better 4 Click Open The file appears as a record at the end of the Hit List 5 To take a record off the hit list right click and select Remove from the context menu Saving files or data sources You can save search results as a file and use this file as a source for searching Saving search results as SDfiles You can save the hit list records as SDfiles using MDL SDfile format You can import SDfiles from ChemBioFinder for Office 13 0 into applications like ChemBioFinder 13 0 Tosave search results in SDfiles sdf format 1 Go to File Export SDFile The Save As dialog box appears 2 Inthe File Name text box type a name for the file 3 Click Save For more information about exporti
15. ng files to other applications see Sending a file to another application on page 7 Saving data sources as DSD files After you complete a search you can save the list of the data sources searched as a Data Source Definition dsd file so that you can search through them again You can use dsd files to search for structures substructures or structures similar to your previous search Tosave the data sources from a search as a dsd file 1 After completing a search go to File Save Source As The Save As dialog box appears 2 Inthe File Name text box type a name for the group of files 3 Click Save The file is saved with a dsd extension Saving lists of directory paths as dsd files 7 Note Only advanced users familiar with text editors should use this procedure You can save lists of directory paths that you search as dsd files You can create these lists with a text editor To save a list of directory paths Open any ASCII text editor Type the directory or database paths you want to search Inthe editor go to File gt Save As The Save As dialog box appears Inthe File Name text box type a name for the file and include a dsd extension for example search1 dsd Click Save Close the editor O oa A W N Searching DSD files To search for a structure in the data sources pointed to by a DSD file Chapter 1 ChemBioFinder for Office 13 0 6 of 19 Ba PerkinElmer For the Better ChemBioFinder f
16. nt tabs to cary out searches Figure 2 3 The Analysis tab 3 Click the Reactant tab s Use Browse to select a ChemBioFinder 13 0 or SDFile database or other source of chemical structures such as a collection of ChemBioDraw files 4 Click Search Combi Enumerator Reaction Analysis Reactant A Enumeration R Search 2 Source size 306 Search hits 4 List size 4 Edit Hitlist Structure source for this component C ChemFinder samples CS_DEMO CFW lt Ok Cancel Figure 2 4 Reactant A You may edit the hit list before continuing a Click Edit Hitlist A message box appears Chapter 2 CombiChem 15 of 19 Da PerkinElmer For the Better ChemBioFinder for Office 13 0 ChemFinder Ultra A To edit the candidate list remove unwanted compounds using Record Omit from List When finished return to ChemFinder For Word by minimizing not closing or exiting the ChemFinder window Figure 2 5 Edit list warning b Click OK to open ChemBioFinder 13 0 To edit the hit list go to Record gt Omit from List 5 Click the Enumeration tab Use Browse to select a database in which to store the results 6 Click Go The results are stored in the database _ Note You can create a new database file by entering a file name 7 Click OK to exit the Combi Enumerator and return to ChemBioFinder for Office 13 0 The results of the enu meration will then be shown as the current hitlist To view the
17. o ore of the following show hide the Standard a select deselect Toolbar menu item toolbar show hide the Status bar select deselect Status bar menu item Chapter 1 ChemBioFinder for Office 13 0 100f19 Ba PerkinElmer For the Better ChemBioFinder for Office 13 0 show the hit list gen select Show List menu item This option is visible only erated during a search when the hit list is hidden hide the hit list gen MA select Hide List menu item This option is visible only erated in a query oper query Re yhen the hit list is visible ation Advanced settings You can customize Commands Toolbars Menus and Keyboard options using the Customize option For example you can assign shortcut keys to any command or remove the shortcut keys assigned to any command To assign a new shortcut key Go to View gt Customize The Customize window appears Select the Keyboard tab Select the menu name from the Category drop down list Select the command to which the shortcut is to be assigned from the Commands list Enter the new shortcut key in the Press New Shortcut Key text box oa A OO N Click Assign and then click Close to exit the Customize window To remove the assigned shortcut key Go to View gt Customize The Customize window appears Select the Keyboard tab Select the menu name from the Category drop down list Select the command from the Commands list Select
18. or Office 13 0 Go to File gt Open The Open dialog box appears Inthe Files of type text box select Data source definitions dsd from the drop down list Inthe File Name text box type the dsd file name or select the file from the list Click Open The first structure in the dsd file appears in the Structure window Click New Search ChemBioFinder for Office 13 0 clears the Structure window Click Edit Structure and draw a structure to find Click Find Now ChemBioFinder for Office 13 0 searches through the files specified in the DSD file Any hits appear in the hit list N DA oO FP W N Sending a file to another application You can send a structure or a file containing structures Such as SD files to another application You can copy a struc ture from an application and paste it into another or you can send multiple structures directly to another application You can send files to any of these applications Microsoft Word Microsoft Excel ChemBioFinder ChemBioDraw ChemACX Com Search To send a hit list to another application 1 Click the Send To menu and choose an application to send the file to The Send To dialog box appears _ Note When you send files to ChemACX Com The Send To dialog box does not appear The current structure is sent directly to ChemACX Com 2 From the Molecules section select one of the following send the current structure displayed in the Structure win Send curren
19. ormula and molecular weight To send a file to ChemBioFinder or ChemBioDraw you must save the file 1 Click the Send To menu and select CS ChemBioFinder or CS ChemBioDraw Files 2 Select the appropriate radio button in the Molecules section and click OK The Save As dialog box appears _ Note Ifa ChemBioFinder cfx file is open you can select it in the Document section of the Send To dialog box 3 Type a name in the File Name text box lt Note To send multiple structures to ChemBioDraw choose a base name for the files For example if there are three molecules in the current hit list and you specify the base name molecule the files will be saved as molecule 1 cdx molecule 2 cdx and molecule3 cdx 4 Click Save If you send a file to ChemBioFinder ChemBioFinder opens and the file you save appears as a form If you send a file to ChemBioDraw a message appears displaying the path of the file you saved Refining your search You can refine your search to increase the chance of finding the structure you want Use the Search tools and the Search Options tab to change your query to refine your search To refine your search Chapter 1 ChemBioFinder for Office 13 0 8 of 19 ChemBioFinder for Office 13 0 I ae Na PerkinElmer For the Better 1 Go to Search gt Restore Previous Query 2 Change your query with the Search Options see the table below 3 Select the files and data sources you want to search 4 Click Find
20. plays all files which match query structure in the hit list window If ChemBioFinder for Office 13 0 finds no hits your search may be too narrow Consider broadening your search options Chapter 1 ChemBioFinder for Office 13 0 9 of 19 Ba PerkinElmer For the Better ChemBioFinder for Office 13 0 Using the search tools Some ChemBioFinder tools used to refine your search can also be used in ChemBioFinder for Office 13 0 To use the search tools select an option from the Search menu or Search toolbar search for the current properties chemical structure chem ical formula molecular weight search for the structure currently displayed in the structure window but ignore any other search properties like molec Find Current Struc ture ular weight restore the previous search so as to modify the search Restore Previous criteria Query see all the records in the search including records Retrieve All without a match to your search For more information about the search tools see the ChemBioFinder User Guide Changing the interface appearance You can change the appearance of the user interface of ChemBioFinder for Office 13 0 You can customize the way the window appears using options available in the View menu You can change some of the display features using the Preferences option Customizing the window To change the appearance of the ChemBioFinder for Office 13 0 window 1 Click the View menu 2 D
21. t molecule dow Send all molecules in current send all the structures listed in the hit list PAKA hit list 3 From the Document section select one of the following if available Chapter 1 ChemBioFinder for Office 13 0 7 of 19 Ba PerkinElmer For the Better ChemBioFinder for Office 13 0 send structures to a new untitled document in an AAE Send molecule s to a new document application send structures to a document you already have Send molecule s to a currently open doc open in an application ument 4 Inthe Document section select the file name from the drop down list if necessary This option is enabled only if you already have a document open in the application If the text box in the Document section is disabled skip this step 5 Click OK If you choose Send To MS Word the structures you send to the application appear in that application as follows a If you select Send all molecules in current hitlist ChemBioFinder for Office creates a table in your document and the molecules in the current hit list along with their molecular formulas weights and source file paths are added to the table a f you select Send current molecule ChemBioFinder Office will export only the structure 7 Note If you need to interrupt a long Send To Word operation bring ChemBioFinder for Office 13 0 to the front and click Stop If you choose Send To MS Excel a spreadsheet is created containing the structure f
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