TerraTox Databases User Manual, vs. 3.1
Contents
1. Name search chemical Formula search CAS number search chemical Structure search and Property search The opening screen of the Search window is shown in Fig 3 showing the main four search capabilities of TerraTox databases Explorer TerraT ox File Edit iew Help Eh Ba SA 53 ho 2 Find chemicals 7 with all of th 4 Search MM Reset SI Reset All Search results F Add search results to existing records Explorer 30948 chemical records Figure 3 Search window overview Name Search Standard Search The Name search standard allows the user to enter up to seven words or word fragments to search the database of choice for all occurrences which contain all of the given word fragments in the chemicals name For example a search for phen amin chlor of the TerraTox Explorer database results in the listing of compounds as shown in Fig 4 Please note that the Name search is not case sensitive 9 Tip The order of text fragments in the search field does not affect the search results TemaT ox 292 g ioj x File Edit View Help Vv te x Cor hy S a t Copy pic Details TerraTax Copyright 2003 TerraBase Inc 30 Module Select Text Search ti Advare seac PA Find chemicals 28 with all of the words phen amin chlor View Reset Reset All Search results 143 records Add2. http www daylight com smiles f_smiles html Kaiser K L E 2003 Neural networks for effect prediction in environmental and health issues using large datasets QSAR Comb Sci 22 185 190 16 Kaiser K L E 1995 Erroneous Data Avenues for Detection and Prevention Editorial Quintessence 1 4 13 16 Kaiser K L E and Niculescu S P 2001 On the PNN modeling of estrogen receptor binding data for carboxylic acid esters and organochlorine compounds Water Qual Res J Canada 36 619 630 2001 http www cciw ca warjc 36 3 36 3 619 htm McKinnon M B and Kaiser K L E 1993 The desktop computer spreadsheet as a scientific database and powerful research tool Chemosphere 27 1159 1169 Acknowledgement TerraBase Inc acknowledges with thanks the contributions of its contractors and associates especially Dr A Krajnc and M B McKinnon to the development of its TerraTox products Security Features As other software providers TerraBase Inc is interested is preventing un authorized duplication and use of its highly sophisticated software products Therefore all copies of this TerraTox program are personalized 1 e they contain encrypted information of the name and affiliation of the rightful user This information is displayed on the Start up screen and can be reviewed at any time by activating the About box prominently displayed on the main program panel see Figure 1 Hence any un authorized propagation o
3. phen amin chlor but rather than requiring all terms to be in each compound to have AT LEAST ONE of the search terms in the name For this option just place the search term in the middle box of the three Advanced Text Search fields Search terms can be changed terms can be added or deleted at will and a new search can be performed with combinations of any of these search conditions In addition the results of one search can be saved and the results of the next search can be appended to the list by activating the Add search results option also shown in Fig 5 Tip The order of text fragments in the WITH AT LEAST ONE or WITHOUT fields does not affect the search results Formula Search Searching by chemical formula is simple and straightforward As shown in Fig 6 formula search can be performed for either a formula fragment sub formula search option or for an exact chemical formula exact formula option Please note that the Formula Search is case sensitive For example searching for r will result in a list of all compounds with Br Cr Sr Zr etc in the chemical formula In contrast search for the letter R will result in compounds containing Rb Rh Ru etc When searching for several 7 atoms simultaneously such Br and Cl in the same compound Hill s rule must be followed and the number of atoms must be specified except for 1 For example searching for compounds with one bromine atom and
4. 971 2 amino 4 chlorophenol 5 chloro 2 hydroxyaniline C6EHECIND 1825 3 amino 4 chlorophenoxpacetic acid 2181 N phenyl 4 4 phenylamino phenyl 4 phenylimino 2 5 cyclohes 3 307 Chlorprocarb 3 methoxycarbonyllaminojpheny 1 chloromethy 204 3245 Basic Yellow 11 Cl 48055 2 2 2 4 dimethoxyphenyllaminojeths 202 3327 Butyrac 2 4 DB 4 2 4 dichlorophenoxy butyric acid dimethylamine OH10CI203 3352 Basic Blue 9 Cl 52015 phenothiazin 5 ium 3 7 bis dimethylamino chloride C16H18CIN35 3368 _ L threo a D galacto octopyranoside methyl chloro 6 7 8 trideoxy 6 1 methyl 4 propyl 2 pyrrolidinyl carbonyljamino 1 thio C25H40CIN208PS 3369 L threo a D galacto octopyranoside methyl 7 chloro 6 7 8 trideoxy 6 1 methyl 4 propyl 2 pyrrolidinyljcarbonyljamino 1 thiom C25H39CI2N208P 3370 L threo a D galacto octopyranoside methyl chloro 6 7 8 trideoxy 3 4 0 1 methylethplidene 6 1 methyl 4 propyl 2 pyrrolidin C28H43CI2N208P 3373 ethanol 2 2 6 13 dichloro 3 10 bis 2 sulfooxyjethyljamino triphenodioxazinediyl bis sulfonyl bis bis hydrogen sulfate feste C26H24CI2KN4Na 3381 methanaminium N 4 2 chloropheny 4 dimethylamino phenyl lmethylene 2 5 cyclohexadien 1 ylidene N methyl sulfate 1 1 C23H25CIN2 gt 4 292 g 20612 chemical records CAP NUM SCRL 2 Figure 5 Advanced Name search A further Name search option is available 1 e to search for several terms such as
5. For using the 3D display please refer to the 3D Viewer section further down While only one of the structure search types can be executed at a time the Accelrys software allows simultaneous search for different atoms in any position when placed into square brackets For example a search for Nclc Br Cl cccc1 will find all aniline derivatives with either ortho bromine or ortho chlorine substituents There is no limit as to the number of different atoms in the square brackets For example a search for Nelc Br Cl I F N O S Se cc O ccl will find all 4 hydroxy aniline derivatives with a chlorine bromine iodine fluorine nitrogen oxygen sulfur or selenium atom in ortho position to the aniline nitrogen atom These substitution rules also apply to cyclic fragments but observe the rules for aromaticity For example a search for nlc c n c c n cl will find all pyridine pyrimidine and 1 3 5 triazine derivatives in the database Tip Due to the relatively slower chemical structure search approximately 10000 compounds minute searching by structure fragment only can be time consuming when checking larger databases such as the TerraTox Explorer database It is therefore recommended wherever possible to combine the structure search with one or more of the other search options In general this will greatly increase the speed of the search 10 TerraT ox 292 g Fiil x File Edit View Help _Text Search Formula S
6. WARRANTY DOES NOT APPLY TO UPDATES FONT SOFTWARE CONVERTED INTO OTHER FORMATS PRE RELEASE BETA TRYOUT PRODUCT SAMPLER OR NOT FOR RESALE NFR COPIES OF SOFTWARE See Section 14 To make a warranty claim you must return the Software to the location where you obtained it along with proof of purchase within such ninety 90 day period If the Software does not perform substantially in accordance with the Documentation the entire liability of TerraBase and your exclusive remedy shall be limited to either at TerraBase s option the replacement of the Software or the refund of the license fee you paid for the Software THE LIMITED WARRANTY SET FORTH IN THIS SECTION GIVES YOU SPECIFIC LEGAL RIGHTS YOU MAY HAVE ADDITIONAL RIGHTS WHICH VARY FROM JURISDICTION TO JURISDICTION For further warranty information please see the jurisdiction specific information at the end of this Agreement if any or contact TerraBase 7 DISCLAIMER THE FOREGOING LIMITED WARRANTY STATES THE SOLE AND EXCLUSIVE REMEDIES FOR TERRABASE S OR ITS SUPPLIER S BREACH OF WARRANTY TERRABASE AND ITS SUPPLIERS DO NOT AND CANNOT WARRANT THE PERFORMANCE OR RESULTS YOU MAY OBTAIN BY USING THE SOFTWARE EXCEPT FOR THE FOREGOING LIMITED WARRANTY AND FOR ANY WARRANTY CONDITION REPRESENTATION OR TERM TO THE EXTENT TO WHICH THE SAME CANNOT OR MAY NOT BE EXCLUDED OR LIMITED BY LAW APPLICABLE TO YOU IN YOUR JURISDICTION TERRABASE AND ITS SUPPLIERS MAKE NO WARRANTIES CONDITIONS REPRESEN
7. display setting to start stop spin of the display etc as shown on the same molecule in Fig 15 Detailed compound information SC view 3D View SMILES clecece CE OieeecclecZIOCC N SCCOCCI Cl GAS 3152 211 HAME 4 2 rorpholin N lethoxy phenyl phenylmethanone hydrochloride FORMULA CISHZACINGS tlt 34 Ad Organisms MOF T cytosol UC mp 120 ER RBA to 40 1 00 ANTI ER relative to tarnoxifen lagti 2 00 0 349 Mote end of record References I Poirot Wi De Medina P Delame F Perie Jal Klaehe A Faye J 0 2000 Synthesis bil Jl Figure 15 Detailed compound information and 3D structure b 14 In order to see a chemical structure in 3D with additional formatting printing and file conversion capabilities simply click on the Details command tab location shown in Fig 9 Activation of Details will open a new larger size window such as shown in Fig 16 This viewer system also has its own Help and Options system Figure 16 3D Viewer display accessible through the Details command Note regarding 3D structures TerraBase Inc cannot guarantee that 3D structures as shown in the Viewer are always displaying the correct R or S form of chiral optically active carbon atoms While most SMILES codes in TerraTox databases have the this information embedded we have noticed that certain canonical 3D SMILES codes are misinterpreted by the SMILES interpreter
8. search results to existing records Name Formula 621 2 4 chlorophenyllethylamine C8H10CIN 971 2 amino 4 chlorophenol 5 chloro 2 hydroxyaniline C6HECIND 1122 2 amino 4 chloro 5 nitrophenol C6HSCIN203 1825 3 arino 4 chlorophenoxyacetic acid C8HSCIND3 2181 N phenyl 4 4 phenylamino phenyl 4 phenylimino 2 5 cyclohexadien 1 ylidene methyl benzeneamine monohydrochloride C37H30CIN3 3077 Chlorprocarb 3 methoxycarbonyllaminojpheny 1 chloromethyl propyllcarbamate C13H17CIN204 3245 Basic Yellow 11 Cl 48055 2 2 2 4 dimethoxyphenyllaminojetheny 1 3 3 trimethyl 3H indolium chloride C21H25CIN202 3327 Butyrac 2 4 DB 4 2 4 dichlorophenoxy butyric acid dimethylamine CIOH10CI203 3352 Basic Blue 9 Cl 52015 phenothiazin 5 ium 3 7 bis dimethylamino chloride C16H18CIN35 3368 _L threo a D galacto octopyranoside methyl chloro 6 7 8 trideoxy 6 1 methyl 4 propyl 2 pyrrolidinylicarbonyljamino 1 thio C25H40CIN208PS 3369 L threo a D galacto octopyranoside methyl chloro 6 7 8 trideoxy 6 1 methyl 4 propyl 2 pyrrolidinyl carbonyljamino 1 thiom C25H39CI2N208P 3370 L threo a D galacto octopyranoside methyl 7 chloro 6 7 8 trideoxy 3 4 0 1 methylethylidene 6 1 methyl 4 propyl 2 pyrrolidin C28H43CI2N208P 3373 ethanol 2 2 6 13 dichloro 3 10 bis 2 sulfooxyjethyllamino triphenodioxazinediy bis sulfonyl bis bis hydrogen sulfate este C26H24CI2KN4Na z gt PA ASA
9. two chlorine atoms in the molecule must be entered as BrCl2 FN TerraT ox 292 g olx File Edit Yiew Help TerraTox Copyright 2003 TerraBase Inc Modula Sel ct Text Search Formula Search CAS Search Structure Search Chemical formula search Hill s rule Search i Formula er View Sub formula search Exact formula search Reset Reset All Search results 980 records Add search results to existing records Name Formula a 3 bromo 1 2 propanediol C3H7Br02 1 bromo 2 propanol C3H7Br0 3 bromo 1 propanol C3H7Br0 4 bromobutyronitrile C4HBBrN 2 bromoethanol C2H5Br0 3 bromopropionitrile C3H4BrN 3 bromopyridine C5H4BrN 2 3 dibromo 1 propanol C3H6Br20 2 bromobenzoic acid C7H56r02 3 bromo 2 2 dimethyl 1 propanol C5H11Br0 2 5 dibromobenzoic acid C7H4Br202 4 bromopyridine hydrochloride C5H5BrCiN bromovaleronitrile CSHSBrN a 292 q 20612 chemical records Figure 6 Formula Search window Tip When searching for compounds with several specific types of atoms present such as bromine chlorine iodine the best method would be to place one of these terms in the Formula search box e g Br and the other ones into the text search box e g chlor iod and perform simultaneously both Text and Formula fields CAS Search Chemical Abstracts Service CAS numbers for chemicals have the formats shown i
10. 292 g 20612 chemical records CAP NUM SCRL 2 Figure 4 Standard Name search Advanced Search The Name search function has an option for an advanced search as also shown in Fig 4 Clicking on the Advanced Text Search option will open the Advanced Text Search window as shown in Fig 5 The Advanced Text Search enables to search simultaneously for compounds WITH ALL of the text fragments WITH AT LEAST ONE of the fragments and WITHOUT certain fragments For example as shown in Fig 5 a search for compounds WITH the word fragments phen amin chlor and WITHOUT the fragment nitro in the name results in the list of compounds shown in the results window Only the first 13 of 135 compounds in the TerraTox Explorer database resulting from above search are visible in the field The rest becomes visible upon scrolling down the right hand scroll bar FN Terral ox 292 g OF x File Edit View Help a amp vy g Copytext Copypic Details Print About TerraTox Copyright 2003 TerraBase Inc Module Select _Text Search Formula Search CAS Search Structure Search V Advanced search ar E ea with all of the words phen chlor amin View at least one of the words without the words nitro Search Reset Reset All Search results 135 records Add search results to existing records Name Formula 621 2 4 chlorophenyllethylamine l C8H10CIN
11. OF ITS SUPPLIERS SHALL BE LIMITED TO THE SUM OF FIFTY DOLLARS U S 50 IN TOTAL 15 This concludes the License Agreement for the TerraTox software If you have any questions regarding this Agreement or if you wish to request any information from TerraBase please use the address and contact information included with this product to contact TerraBase Gen WWCombined USEnglish 8 7 00 11 14 Trademarks and Copyrights Windows 95 Windows 98 Windows NT Windows 2000 Windows ME and Windows XP are trademarks of Microsoft Corporation Redmond Washington USA Other copyrights and trademarks are those of their respective owners Technical Requirements Operating system PC with Windows 98 NT 2000 ME or XP operating system Central processor unit CPU No specific requirement duration of searches will vary with hard disk and CPU speed 2 0 GHz or higher CPU recommended Mouse or other pointing device required Screen setting Variable 800 x 640 or higher recommended CD ROM drive required Other Presence of the TerraTox CD in the CD ROM drive is required for program execution 22 Installation Instructions The TerraTox software is a fully functional stand alone system easy to install or uninstall It consists of four installation parts we recommend installation in the order given below Before proceeding with the installation please print the Readme txt file in the root directory of the TerraTox CD for important installati
12. OUNT YOU ORIGINALLY PAID IF YOU A DO NOT USE THE SOFTWARE AND B RETURN IT WITH PROOF OF PAYMENT TO THE LOCATION FROM WHICH IT WAS OBTAINED WITHIN THIRTY 30 DAYS OF THE PURCHASE DATE 1 Definitions Software means a all of the contents of the files disk s CD ROM s or other media with which this Agreement is provided including but not limited to 1 TerraBase Inc or third party computer information or software 11 digital images stock photographs clip art sounds or other artistic works Stock Files 111 related explanatory written materials or files Documentation and b upgrades modified versions updates additions and copies of the Software if any licensed to you by TerraBase Inc collectively Updates Use or Using means to access install download copy or otherwise benefit from using the functionality of the Software in accordance with the Documentation Permitted Number means one 1 unless otherwise indicated under a valid license e g volume license granted by TerraBase Inc Computer means an electronic device that accepts information in digital or similar form and manipulates it for a specific result based on a sequence of instructions TerraBase means TerraBase Inc a Canadian corporation 1063 King St West Suite 130 Hamilton Ontario L8S 483 CANADA 2 Software License As long as you comply with the terms of this End User License Agreement the Agreement TerraBase grants to yo
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14. TerraTox Databases User Manual vs 3 1 Copyright 2006 TerraBase Inc Software Purpose TerraTox is a specialized database software designed and optimized solely for the quick retrieval of available toxicological and physico chemical data for chemical substances TerraTox database modules contain between 1 000 and 100 000 individual chemical substances each The available information for each substance varies but up to 250 different types of data are available for the more common compounds References are shown for the more significant properties Chemical structures are shown in 2D or 3D user determined The TerraTox software has the most powerful search routines available in the industry allowing simultaneous search by chemical structure name formula CAS and any two of the up to 250 types of effects listed in the specialized TerraTox databases This search ability results in unparalleled speed convenience and success in finding the information sought TerraTox Database Modules At this time the following TerraTox modules are available For details on the databases below please see the TerraBase web site or use the hyperlinks below TerraTox Drugs TerraTox Explorer TerraTox HIV 1 TerraTox Pesticides TerraTox Tetrahymena TerraTox Skin TerraTox Steroids RBA TerraTox Vibrio fischeri New and expanded modules will come on stream from time to time Please check ou
15. already TerraTox databases employ highly sophisticated search systems that allow the simultaneous searching by several search types namely name formula CAS structure and property search All what is required is entering the desired search parameters into the various fields and a click on the Search button When performing any search the search status window will appear and inform the user about the type s of search which is are under way the search progress approximate time remaining and the total number of compounds identified so far An example 1s shown in Fig 12 Search in progress please wait Search status Structure search is INACTIVE Formula search is INACTIVE Name searchit INACTIVE CAS searchis INACTIVE Property search is ACTIVE 4 seconds remaming 492 records found Figure 12 Search status window Tip After performing a search with for example three simultaneous search types if the user decides to drop one of these search types it is best to use the Reset button for that field in order to avoid searching for an empty field 3D Viewer In addition to the 2D Viewer of the chemical structures automatically activated whenever there is information presented to it for some compounds or mixtures no structure is shown the TerraTox system has a built in 3D Viewer The latter can be activated at any time when there is a structure shown in the 2D viewer window by click
16. ducts in most cases free of charge Contact our help department with any question and concern about our products either by EMAIL FAX or MAIL TerraBase Inc 1063 King St West Suite 130 Hamilton ON L8S 4S3 Canada Fax 905 527 0263 Internet http www terrabase ca Copyright 2006 TerraBase Inc 23
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18. e feedback to TerraBase regarding testing and use of the Pre release Software including error or bug reports If you have been provided the Pre release Software pursuant to a separate written agreement such as the TerraBase Incorporated Serial Agreement for Unreleased Products your use of the Software is also governed by such agreement You agree that you may not and certify that you will not sublicense lease loan rent or transfer 21 the Pre release Software Upon receipt of a later unreleased version of the Pre release Software or release by TerraBase of a publicly released commercial version of the Software whether as a stand alone product or as part of a larger product you agree to return or destroy all earlier Pre release Software received from TerraBase and to abide by the terms of the End User License Agreement for any such later versions of the Pre release Software Notwithstanding anything in this Section to the contrary if you are located outside Canada or the United States of America you agree that you will return or destroy all unreleased versions of the Pre release Software within thirty 30 days of the completion of your testing of the Software when such date is earlier than the date for TerraBase s first commercial shipment of the publicly released commercial Software 14 4 Tryout Product Sampler NFR Additional Terms If the product you have received with this license is a tryout product sampler or NFR copy of the Softwar
19. earch CAS Search Structure Search Chemical structure search Chemical structure in SMILES format eleceec 1CCCO Fragment identified as a sub structure Exact chemical structure match 7 Fragment NOT identified as a sub structure Molecular structure similarity Tanimoto Search Reset Search results Reset All Name Formula 292 g 20612 chemical records Figure 9 Chemical structure search window with SMILES string Property Search The TerraTox search system also allows for the search of numeric values and text conditions in any of the data fields Each TerraTox database has its own list of effect and property fields which are seen in First property and Second property scrollable windows The following examples are from the Explorer database On activating the Property search tab as shown in Fig 3 the Property Search window will appear as shown in Fig 10 The identical lists of searchable properties can be scrolled and one parameter field can be selected from each list As the lists contain both fields with numeric values such as toxicity values in pT notation and text fields such as the Use effect field the search options available will change accordingly For example clicking on a text only search term such as the Use effect line in the First property window will result in the Value searc
20. ed compound information and 2D structure 0 0 0 ccccccccccccceeeeeeeeeeeeeees 14 Figure 14 Detailed compound information and 3D structure a 0 cccceeeeeeeeeeeees 14 Figure 15 Detailed compound information and 3D structure b 0 0 ccceeeeeeeeeeees 14 Proure LO SD VIeWer GISplay axccieot gas sateeics cdianeeretens ace tesateuais eco eee nee ee 15 List of Tables Table 1 Valid and invalid examples of Accelrys SMILES code e 16 Introduction Welcome to the TerraTox databases a series of unique database software modules which can simultaneously be searched by name chemical formula CAS number chemical structure or fragments thereof and up to two concurrent field values numerical or text TerraTox databases have been developed by TerraBase Inc TerraTox database products are designed for easy use and provide the most important information for chemicals from the relevant scientific literature They are maintained and updated regularly by reference to the most recent publications TerraTox database products are valuable research tools in the fields of health environment pharmaceuticals and general chemistry Opening Window The TerraTox module will display the initial TerraBase Inc logo and its address the user name and affiliation the copyright and related information This screen 1s normally visible for a few seconds only upon accessing the software but can also be accessed anytime from the Help Abo
21. er The search window for chemical structure fragments is shown in Fig 8 The chemical structure search window has four search options namely FRAGMENT present EXACT STRUCTURE FRAGMENT absent and SIMILARITY Tanimoto similarity function selectable from 0 to 100 similarity In contrast to the text search only one of these four structure search types can be executed at any time however the chemical structure search can be combined with an un restricted number of the other search functions including advanced text formula and CAS searches which results in extremely powerful and fast searches of the TerraTox databases TerraTox 292 e Iof x File Edit View Help ops etails About TerraTox Copyright 2003 TerraBase Inc _Text Search Formula Search CAS Search Structure P Chemical structure search Chemical structure in SMILES format Fragment identified as a sub structure Exact chemical structure match Fragment NOT identified as a sub structure Molecular structure similarity Tanimoto rh Reset Formula Ready 292 e 20612 chemical records Figure 8 Chemical structure search window Whenever a valid SMILES string is entered into the SMILES string field a chemical graph will automatically appear in the window to the right This is shown on the example of n butylbenzene with the SMILES string cl ccecc 1CCCC in Fig 9
22. f this software can be traced back to the original source Anyone knowing of any such un authorized copies is requested to contact TerraBase Inc We offer generous rewards for information of any illegal duplication or use of this program as described in the About box In order for the TerraTox program to function properly the TerraTox CD has to be present in a CD ROM drive on the computer system which is used to run the program Other than for archival copies to be used solely for backup and protection against loss by the rightful user duplication of this software is not permitted 17 Legal License Agreement The rightful TerraTox user is hereby granted a non exclusive use license subject to the agreement as described in the text below TerraTox End User License Agreement NOTICE TO USER PLEASE READ THIS CONTRACT CAREFULLY BY USING ALL OR ANY PORTION OF THE SOFTWARE YOU ACCEPT ALL THE TERMS AND CONDITIONS OF THIS AGREEMENT INCLUDING IN PARTICULAR THE LIMITATIONS ON USE CONTAINED IN SECTION 2 TRANSFERABILITY IN SECTION 4 WARRANTY IN SECTION 6 AND 7 LIABILITY IN SECTION 8 AND SPECIFIC EXCEPTIONS IN SECTION 14 YOU AGREE THAT THIS AGREEMENT IS ENFORCEABLE LIKE ANY WRITTEN NEGOTIATED AGREEMENT SIGNED BY YOU IF YOU DO NOT AGREE DO NOT USE THIS SOFTWARE IF YOU ACQUIRED THE SOFTWARE ON TANGIBLE MEDIA e g CD WITHOUT AN OPPORTUNITY TO REVIEW THIS LICENSE AND YOU DO NOT ACCEPT THIS AGREEMENT YOU MAY OBTAIN A REFUND OF THE AM
23. h text number window to become active together with the Case sensitive window When clicking on a numeric value only search term such as FHM 96 pT fathead minnow 96 hr LC50 in log L mmol units the Value search text number will become active together with the Condition window The numeric condition available are 1 equal to 11 greater than or equal to gt and 111 lesser than or equal to lt 11 Name Search Formula Search CAS Search Structure Search Property Search L m First property p Second property Vale sealbh tevteAumne onal Reset All Formula Figure 10 Property search window An example of a single numeric property search is shown in Fig 11 Searching for values with FHM 96 pT for a value of 5 and the condition gt will result in a list of more than 900 compounds as shown in Figure 11 _Name Search Forn m First property CATF 96 pT FHM 96_ mg L FHM 96 pT TerraQSAR FHM 1 1 32d pT ext number 5 Condition 4 Search 0 Reset Search results 935 records _NNe Formula 21 Wetrachloride CCl4 27 anide CNNa 46 C2CI6 C2HogN2S2 gt mercury I thiocyanate Figure 11 Property search result 12 Simultaneous Search of Two or More Fields As mentioned
24. ing on the 3D tab shown in the enlargements in Fig 13 2D and Fig 14 3D 13 Detaled compound information 2D view ap view EMILES cleeeee 1 OE Oieee ACCN CCTC CAS T3221 HAME 4 2 rorpholin N lethoxy phenyl pherylmethanone hydrochloride FORMULA CISH22CINOS tlt SF oe Organisms MOF T cytosol QC mp 120 ER RBA to 40 1 00 ANTI ER relative to tarnoxifen lagti 2 00 0 34 Mote end of record References i Poirot ht De Medina P Delame F Perie Jal Klaebe A Faye J C 2000 Synthesis bil F NM i d Figure 13 Detailed compound information and 2D structure Detailed compound information SMILES elecece CE OeeecclecZIOCC N CCOCCI Cl CAS T 3132 71 HAME 4 2 rorpholin N lethoxy phenyl pherylmethanone hydrochloride FORMULA CIHeACINOS tlt SF oe Organismal MOF T cytosol QC mp 120 ER RBA to 40 1 00 ANTI ER relative to tarnoxifen log T04 200 0 Mote end of record SD view 3D View 1 Poirot M De Medina Po Delarue F Pere Jad Klaebe AL Faye J C 2000 Synthesis bi lal Figure 14 Detailed compound information and 3D structure a The default display of the 3D display is set to ball and stick but this setting can easily be changed by placing the cursor into the 3D window and using a right click of the mouse button This will open a drop down window to change the
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26. is Agreement and any other terms and conditions upon which you legally purchased a license to the Software Notwithstanding the foregoing you may not transfer education pre release or not for resale copies of the Software 5 Updates If the Software is an Update to a previous version of the Software you must possess a valid license to such previous version in order to Use the Update You may continue to Use the previous version of the Software on your computer after you receive the Update to assist you in the transition to the Update provided that the Update and the previous version are installed on the same computer the previous version or copies thereof are not transferred to another party or computer unless all copies of the Update are also transferred to such party or computer and you acknowledge that any obligation TerraBase may have to support the previous version of the Software may be ended upon availability of the Update 6 LIMITED WARRANTY Except as may be otherwise provided in Section 14 TerraBase warrants to the person or entity that first purchases a license for the Software for use pursuant to the terms of this license that the Software will perform substantially in accordance with the Documentation for the ninety 90 day period following receipt of the Software when used on the recommended hardware configuration Non substantial variations of performance from the Documentation does not establish a warranty right THIS LIMITED
27. lt lower case c formerly only interpreted as sp carbon is now interpreted as either as sp or sp carbon depending on its surrounding and connections to other atoms The determinant here is whether or not the carbon atom is part of an aromatic ring as defined by the Hueckel rules This has ramifications for the correct interpretation of SMILES strings by the TerraTox programs as they are built on the backbone of the Accelrys software Therefore all users are cautioned to ascertain that their SMILES codes follow the rules of the Accelrys software i e to ascertain that only sp carbons in ring systems which satisfy Hueckel conditions for aromaticity are given in lower case c all other sp carbons whether in rings or not must be entered as capital C together with the appropriate double bond symbols Some examples of valid and not valid SMILES strings are listed below in Table 1 Table 1 Valid and invalid examples of Accelrys SMILES code Substance SMILES invalid SMILES valid cyclopentadiene cleccCl C1 CC CC1 coumarin clec2OC O cce2ccl clec2OC O C Ce2ccl The SMILES strings shown as invalid are valid per se however the interpretation of these codes by the Accelrys system are the hydrogen saturated compounds cyclopentane and 3 4 dihydrocoumarin respectively Literature Accelrys Inc 2002 http www accelrys com Daylight Chemical Information Systems Inc 2002 SMILES Tutorial
28. n for damages you have incurred under or in connection with this Agreement only if the damage has been caused by the willful or grossly negligent act of TerraBase or its agents TerraBase is liable only to the extent of the typically foreseeable damage for such damages which have been caused by any other negligent breach of a substantial contractual duty by TerraBase or its agents These aforementioned limitations apply irrespective of their legal basis in particular with regard to any pre contractual or auxiliary contractual claims The limitations shall not apply however to any mandatory liability under the applicable German or Austrian Product Liability Act nor to any damage which is caused due to the breach of an express warranty to the extent that such express warranty was intended to protect the user against the specific damage incurred The obligations under the second sentence shall not apply if any damage is caused by your having altered the Software or if the respective data carriers media have been damaged by accident misuse or inappropriate use or if the damage concerned has been caused by the use of the Software in connection with other software for which the Software was not designated to be used according to the Documentation 14 3 Pre release Product Additional Terms If the product you have received with this license is pre commercial release or beta Software Pre release Software then the following Section applies To the extent
29. n the CAS Search window Fig 7 It allows to search for compounds with known or partially known CAS numbers First select the appropriate mask 21 11 1 311 11 1 etc and then fill in the available information or use question marks for missing information For example a search for 111 would find all compounds in the database with CAS numbers starting with 111 The maximum number of question marks for unknown and higher in the specified database FA TerraTox 292 g or File Edit View Help ag S vy amp E Copytext Copypic Details TerraTox Copyright 2003 TerraBase Inc Module Select Text Search Formula Search CAS Search Strictine Search gt CAS registry number search Search CAS mask type CAS number B 21114 view C 3114114 C 411111 C 51111 11 1 C 611111114 Search Reset Reset All Search results 980 records Add search results to existing records Formula 292 q 20612 chemical records Figure 7 CAS Search window Structure Search TerraTox modules use as chemical structure input a chemical s SMILES code 2D or 3D which is an international code for the representation of chemical structures and amenable to computer analysis Numerous chemical structure editors are available freely on the internet and can be used to create or transfer molecular structures into SMILES code including the built in 3D View
30. of the Viewer and get switched from one e g R to the other e g S form For structures where the correct 3D information may be critical such as peptide like compounds we recommend using a different 3D viewer such as the ChemAxon program MarvinView The latter is available for free download after free registration from ChemAxon at In order to get the correct 3D structure picture of a canonical SMILES code provided in a TerraTox database use the Copy text command and copy the entire compound information to any text editor Then copy from there the SMILES string only open the MarvinView program and Edit Paste the SMILES string into it In our experience the MarvinView program has always provided the correct R S structure information 15 SMILES Notation The Simplified Molecular Input Line Entry System SMILES has been developed by D Weininger at the beginning of the 1980 s It is far superior to the previously used Wiswesser Line Notation WLN for coding and depicting chemical structures by being simple intuitive and machine readable For an excellent tutorial on the SMILES notation refer to the Daylight Corp web site Recently Accelrys Inc introduced a variety of software modules allowing the visualization of SMILES codes as chemical structure drawings In this process Accelrys introduced changes to the common Daylight Corp interpretation of SMILES codes by their software As a resu
31. official languages are written in either an ideographic script e g hanzi kanji or hanja and or other script based upon or similar in structure to an ideographic script such as hangul or kana or c the Netherlands if a license to the Software is purchased when you are in any other jurisdiction not described above The respective courts of Ontario when Canadian law applies Tokyo District Court in Japan when Japanese law applies and the courts of Amsterdam the Netherlands when the law of the Netherlands applies shall each have non exclusive jurisdiction over all disputes relating to this Agreement This Agreement will not be governed by the conflict of law rules of any jurisdiction or the United Nations Convention on Contracts for the International Sale of Goods the application of which is expressly excluded 11 General Provisions If any part of this Agreement is found void and unenforceable it will not affect the validity of the balance of the Agreement which shall remain valid and enforceable according to its terms This Agreement shall not prejudice the statutory rights of any party dealing as a consumer This Agreement may only be modified by a writing signed by an authorized officer of TerraBase Updates may be licensed to you by TerraBase with additional or different terms This is the entire agreement between TerraBase and you relating to the Software and it supersedes any prior representations discussions undertakings communicat
32. on information and carefully follow the recommendations given therein Part 1 Adobe software To install the Adobe Reader program vs 5 05 which is required to read the TerraTox Manual accessible from the F1 key or from the TerraTox Help menu use the Windows Control Install Remove Software command to run the arSOSenu exe in the Adobe folder and follow the instructions Part 2 Accelrys software To install un install the Accelrys supporting software necessary for the proper functioning of the TerraTox program use the Windows Control Install Remove Software command to run each of the exe files in the Accelrys folder See the Readme txt file for detailed installation instructions Part 3 Viewer software To install un install Viewer supporting software necessary for the proper functioning of the TerraTox program use the Windows Control Install Remove Software command to run each of the exe files in the Viewer folder See the Readme txt file for detailed installation instructions Part 4 TerraTox software To install un install the TerraTox software follow the instructions in the Readme txt file Customer Support TerraBase Inc is committed to effective customer support With the rapid change in PC technology operating systems and other software and hardware changes the occasional hiccup is bound to happen We will try our best to help customers with problems related to our pro
33. ou are permitted to make pursuant to this Agreement must contain the same copyright and other proprietary notices that appear on or in the Software Without exception you agree not to modify adapt or translate the Software You also agree not to reverse engineer decompile disassemble or otherwise attempt to discover the source code of the Software Trademarks shall be used in accordance with accepted trademark practice including identification of trademarks owners names Trademarks can only be used to identify printed output produced by the Software and such use of any trademark does not give you any rights of ownership in that trademark Except as expressly stated above this Agreement does not grant you any intellectual property rights in the Software 4 Transfer You may not rent lease sublicense or authorize all or any portion of the Software to be copied onto another users computer except as may be expressly permitted herein You may however transfer all your rights to Use the Software to another person or legal entity provided that a you also transfer each this Agreement the Software and all other software or hardware bundled or pre installed with the Software including all copies Updates and prior versions and all copies of font software converted into other formats to such person or entity b you retain no copies including backups and copies stored on a computer and c the receiving party accepts the terms and conditions of th
34. r web site or send an email message with a request to be informed on specific developments TerraQSAR Computation Modules Our valued customers are also advised on the concurrent development of our TerraQSAR computation programs For details please see the TerraBase web site Table of Contents na 0 M6126 ah PUTDOSC ee ee a ee l TerraTox Database Modules c ccccsccscssssssssceceesesesesessececscacavavsvevscsesesesscsessasavaveveee l TerraQSAR Computation Modules c c ccccccccscsssssesesecesessecececsvscecscscecececeecavevavavecaeaceees l TapE OTE Cll CCM ae tai syahsee idol stonotdaasdoatgeyinie wat seeeoeseotdaasteaigecnnet es 2 LISCO E IOUN Serer outa Asesinas Gee Ase eas at 2 EAST OE TIDIG S erain A esos tedmeaeeh orceneeaeee een eases 2 Introdu Osace dans E E A a S 3 OPENDE W MAON orrn a oes oe eed he eN 3 Module SOLE CE eer aea E R Deaan E R DOEA an ATO 4 DG ARC NINE viser n A 4 Name SeaTe Desreionon n E aA a a 5 Formula Scare i encare a e aoe ne 7 CASOS ea ee een sen nite armenia erat eee een somata armen Sea ete eee een smn arr a ares 8 SUC TUNES SCAR CL hs ecco conces ight alee ceed aa eat concn elena atc ES 9 POS ye A aah eat a erheshains Netnaened e aces aaeee 11 Simultaneous Search of Two or More Fields iscicseissicscictiencmnavbtanetcs eacieesiieteeenteiadans 13 Bel VEO WCU ass ccohiauie scdasauceneeaussesscewen vases onedaveusesratseene scence acenone au ausoevauusse suse sastanoneds 13 NOE Tee ardine SI SIrUCWITES ara
35. ra E ea rectaecet maton eee ueeiak 15 SMILES NOAHO Neen set ela Pan ah nahn at Pasa at neta ee eet 16 PS AL LS osre suns dei a dajunit vs uctoniseurde dances e e a aO 16 PACKMOW ICC CCINC I mannes na teases ee ietont N A N 17 De CUTIDY F CAUITCS ctscetatauutcctiadnsdiuiud a a aa 17 DSM sess A EE EE ys bahia ao E ch as E ees E E A E A E E E E 18 icense AGTE Mon esnai e E EA O EO 18 Trademarks and COPY TGS sic sts csscn css co sie iiccsccwt los EE E E EE EE 22 Technical REQUIT CMIC IS 5 sisasnckscuctrnadesecesncebedisastsaatinndsesoundidaseuandesendeaiosacunndesuededdsawensnceets 22 l stallanon INSUUCTIOMS o T ee cesnaaaeeeestaned 23 CUSTOMICH SUPPOL zerrien iina T E 23 List of Figures Figure 1 Tetra lox opening windOw sereinasenon tanin aa A Eai 3 Fieu 22 Module Selecion Dox rara ENS 4 Figure 3 Scared WindOw OVE VION aa a E O NE AE 5 Proure Sandard Names arc Mencnrenion a a ee 6 Fisoo Advanced Nime Sedar Mina veteccsiiuress nein onseisaces ya a a NS 7 Figure G kormila Search WitGOw sirai aen e a a E 8 Figure 7e CAS Search Wind Ow serrin rosina n E ea 9 Figure 8 Chemical structure search Window essrsisnrissiinseata a a a a 10 Figure 9 Chemical structure search window with SMILES string cc ecceeeeeeees 11 Fieure LO Property searc E WNdONosnsrenis A 12 Fisure Ll Property searc hirestlte airneisi a ea E N EE ROERE EREE 12 Figure 12 Search stats WMO W axcteocassucecusinsdsweteandevcuseseracedodeceusis REEE A 13 Figure 13 Detail
36. reement but in no other respects and for no other purpose For further information please see the jurisdiction specific information at the end of this Agreement if any or contact TerraBase 9 Export Rules You agree that the Software will not be shipped transferred or exported into any country or used in any manner prohibited by the any law governing such activities either in Canada or the United States such as the United States Export Administration Act or any other export laws restrictions or regulations collectively the Export Laws In addition if the Software is identified as export controlled items under the Export Laws you represent and warrant that you are not a citizen or otherwise located within an embargoed nation including without limitation Iran Iraq Syria Sudan Libya Cuba North Korea and Serbia and that you are not otherwise prohibited under the Export Laws from receiving the Software All rights to Use the Software are granted on condition that such rights are forfeited if you fail to comply with the terms of this Agreement 10 Governing Law This Agreement will be governed by and construed in accordance with the substantive laws in force a the Province of Ontario if the license to the Software is purchased when you are in Canada the United States Canada or Mexico or b in Japan if a license to the Software is purchased when you are in Japan China Korea R O C or other Southeast Asian country where all
37. son or entity that first purchases a license for the Software that the Software will perform substantially in accordance with the Documentation for a period of six 6 months following receipt of the Software when used on the recommended hardware configuration Non substantial variations of performance from the Documentation does not establish a warranty right THIS LIMITED WARRANTY DOES NOT APPLY TO UPDATES FONT SOFTWARE CONVERTED INTO OTHER FORMATS PRE RELEASE TRYOUT PRODUCT SAMPLER NOT FOR RESALE NFR COPIES OF SOFTWARE OR TO SOFTWARE THAT HAS BEEN ALTERED BY YOU TO THE EXTENT SUCH ALTERATIONS CAUSED A DEFECT To make a warranty claim you must return the Software at our expense to the location where you obtained it along with proof of purchase within such six 6 month period If the Software does not perform substantially in accordance with the Documentation the entire liability of TerraBase and your exclusive remedy shall be limited to either at TerraBase s option the replacement of the Software the reduction of the license fee or a refund of the license fee you paid for the Software THE LIMITED WARRANTY SET FORTH IN THIS SECTION GIVES YOU SPECIFIC LEGAL RIGHTS For further warranty information please contact TerraBase 14 2 Limitation of Liability for Users Located in Germany and Austria If you purchased a license to the software in Germany or Austria then Section 8 does not apply instead TerraBase may be liable without limitatio
38. that any provision in this Section is in conflict with any other term or condition in this Agreement this Section shall supercede such other term s and condition s with respect to the Pre release Software but only to the extent necessary to resolve the conflict You acknowledge that the Software is a pre release version does not represent final product from TerraBase and may contain bugs errors and other problems that could cause system or other failures and data loss Consequently the Pre release Software is provided to you AS IS and TerraBase disclaims any warranty or liability obligations to you of any kind WHERE LEGALLY LIABILITY CANNOT BE EXCLUDED FOR PRE RELEASE SOFTWARE BUT IT MAY BE LIMITED TERRABASE S LIABILITY AND THAT OF ITS SUPPLIERS SHALL BE LIMITED TO THE SUM OF FIFTY DOLLARS U S 50 IN TOTAL You acknowledge that TerraBase has not promised or guaranteed to you that Pre release Software will be announced or made available to anyone in the future that TerraBase has no express or implied obligation to you to announce or introduce the Pre release Software and that TerraBase may not introduce a product similar to or compatible with the Pre release Software Accordingly you acknowledge that any research or development that you perform regarding the Pre release Software or any product associated with the Pre release Software is done entirely at your own risk During the term of this Agreement if requested by TerraBase you will provid
39. u a non exclusive license to Use the Software for the purposes described in the Documentation Some third party materials included in the Software may be subject to other terms and conditions which are typically found in a Read Me file located near such materials 2 1 General Use You may install and Use a copy of the Software solely on your compatible personal computer Server Use You may not install the Software on a computer file server for the purpose of downloading installing or using the Software onto or with other computers 2 3 Backup Copy You may make one backup copy of the Software provided your backup copy is not installed or used on any computer You may not transfer the rights to a backup copy unless you transfer all rights in the Software as provided under Section 4 3 Intellectual Property Rights The Software and any copies that you are authorized by TerraBase to make are the intellectual property of and are owned by TerraBase Incorporated and its suppliers The structure organization and code of the Software are the valuable trade secrets and confidential information of TerraBase Incorporated and its suppliers The Software is protected by copyright including without limitation by Canadian and United States Copyright Law international treaty provisions and applicable laws in the country in which it is being 18 used You may not copy the Software except as set forth in Section 2 Software License Any copies that y
40. ut menu item as shown on Fig 1 Location of Module Select Search and View functions are shown as well as the Help About command location TerraTox 292 e File Edit View Help Ea Copy text Copy pic Details lel Es TerraTox Copyright 2003 TerraBase Inc tg Module Select p Search Structure Search View b all of the words Reset Reset ll Search results I Add search results to existing records Name Formula Ready 292 e 20612 chemical records CAP NUM SCRL Figure 1 TerraTox opening window Module Select For users subscribing to two or more databases upon clicking on the Module Select icon a list of available choices will appear as shown in Fig 2 the list of modules available depends on the user s subscription choices The main field shows currently available modules ER Explorer DEMO TerraTox Sel File Edit Yiew Help Available TerraTox modules Explorer DEMO TerraBase Inc Advancing your R amp D with innovative sofiware Databases TerraTox Drugs TerraTox Explorer TerraTox HIV 1 TerraTox Pesticides TervaTox Skin TerraTox Steroids RBA TerraTox Tetrahymena TerraToxs Vibrio fischeri Explorer DEMO 57204 chemical records Figure 2 Module Selection box Searching The TerraTox programs have a variety of search functions built in They include main functions only
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