USER MANUAL - Bioinformatics.Org
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1. File Help Step 4 Performing Comparison Fingerprinting Query File 3357 ms Formatting Database Library Oms Fingerprinting Database File 3338 ms Indexing Database 239 ms Formatting Query Library 107 ms Comparing Output 1vs1 1 0 2vs 2 1 0 3vs 3 1 0 4vs 4 1 0 783 vs 4 0 9805825242718447 Search Time 6958497 ns Hash Time 547374ns Prune Time 0 ns Compare 6000 Baseline Memory Use 9832 KB AD OOO A Finished The last pane will show you ChemCom s progress as it performs the comparison After each step it will show you how long that respective process took2. USER MANUAL ChemCom a Software Program for searching and Comparing Chemical Libraries Sirus Saeedipour David Tai Jianwen Fang Contact jianwen fang nih gov Availability ChemCom can be run as either a JWS application via this link http www bioinformatics org chemcom launchChemCom jnlp or a desktop Java application by downloading the whole package here If you choose the second option we recommend NetBeans V7 or up to compile and execute ChemCom 86800 Java Application Blocked Application Blocked by Java Security oe For security applications must now meet the requirements for the High or Very High security settings or be part of the Exception Site List to be allowed to run More Information Name chemcom ChemComApp Location http bioinformatics org Your security settings have blocked a self signed application from running Reason Depending on the security settings of your computer your computer may block ChemCom from running because it is a self signed application see above You may need to change Java security settings by adding bioinformatics org to the exception site list see below You should save the lauchChemCom jnlp file to your computer and then open it using right mouse e090 Java Control Panel General Update Java Security Advanced v Enable Java content in the browser Security level for applications not on the Exception Site list Very High Only Java applications i
3. dentified by a certificate from a trusted authority are allowed to run and only if the certificate can be verified as not revoked High Java applications identified by a certificate from a trusted authority are allowed to run even if the revocation status of the certificate cannot be verified Exception Site List Applications launched from the sites listed below will be allowed to run after the appropriate securi rompts Edit Site List http bioinformatics org Restore Security Prompts Manage Certificates ok Cancel Apply Step by step Execution Step 1 Selecting Input Files File Help Step 1 Select Input Files oso fe tape Database SDF File Browse Tags v _ Use Database ChemCom File Browse Instructions Please select the Structure Data Files SDFs you wish to compare If you are wanting to output the results of the comparison as a CSV file select the loaded tags once you select a SDF file If you have a ChemCom file in place of a standard SDF file you may select it as your Database However if you wish to output the results of the comparison to a CSV file or SDF files as shown in Step 3 you will not be able to use those output options Additionally once you load a ChemCom file the configuration information for the comparison that was used to create the ChemCom file will automatically be loaded shown in Step 2 and you will be unable to chan
4. e used for the current comparison The description of SymDex algorithm can be found at http pubs acs org doi pdf 1 0 102 1 ci200606t e Enabling Keep Intermediate Files will allow ChemCom to store intermediate files that are calculated by ChemCom on the computer you are using to be reused thus avoiding unnecessary recalculations and significantly reducing comparison times when the same SDF files are loaded in future comparisons Step 3 Selecting Output Options File Help Step 3 Select Output Options _ Output CSV File Save Location Browse __ Output SDF Files Query SDF Browse Database SDF Browse _ Output Database as ChemCom File Save Location Browse Previous Peform Comparison The last step prior to performing the actual comparison is to select locations and names for the output files Four output files can be saved The output CSV file has three columns two for the query and database chemical tags and the third is for Tanimoto scores Each row represents a pair of chemicals with similarity above the threshold chosen in the previous step The structures of the distinct chemicals in the CSV file can be saved in the output SDF files In addition the database can be saved as a binary ChemCom file This file can be reused for searching the same database using the same algorithm and parameters in future Thus reduce the time to run searches Step 4 Performing the Comparison
5. ge the paramters Note Currently ChemCome files cannot be used as the Query This feature may be added in future versions of ChemCom Previous Next Upon opening ChemCom you are prompted this window which presents you with Step 1 For this step you must browse and select your Query and Database SDF Files File Help C UsersVohnSmith Desktop query sdf chemical_name CAS_number _ Use Database ChemCom File iniiai supplier_tag supplier_id Database SDF File Instructions Please select the Structure Data Files SDFs you wish to compare If you are wanting to output the results of the comparison as a CSV file tags once you select a SDF file If you have a ChemCom file in place of a standard SDF file you may select it as your Database However if you wish to output the results of the comparison to a CSV file or SDF files as shown in Step 3 you will not be able to use those output options Additionally once you load a ChemCom file the configuration information for the comparison that was used to create the ChemCom file will automatically be loaded shown in Step 2 and you will be unable to change the paramters Note Currently ChemCome files cannot be used as the Query This feature may be added in future versions of ChemCom Previous Next Upon loading a SDF file all SDF tags of the respective SDF file are displayed Here you need to select which tags you want your output file
6. s to use as seen in Step 3 These tags should be unique for each chemical Optionally you may choose to use a Database ChemCom file to supplement your Database SDF file Doing so will considerably speed up your comparison at the cost of limiting your comparison options as seen in Step 2 Step 2 Selecting Algorithm Details File Help Step 2 Select Algorithm Details Algorithm Mode UnionBit Algorithm B Fingerprinting Algorithm FP2 Min Tanimoto Threshold 0 9 Maximum Value 13 V Preprocessing _ Keep Intermediate Files Instructions First select one of the four algorithms to use for your comparison Second please select the molecular fingerprinting algorithm you would like to use The SDF files must be parsed using a fingerprinting algorithm in order to encode molecular structures in a series of bits for easier processing FP2 indexes linear fragments up to 7 atoms MACCS utilizes SMARTS patterns specified in the file MACCS tt Previous Next The next step involves choosing the desired comparison algorithm along with its parameters Additional information regarding the different fingerprinting algorithms are shown as tooltips and shown at the bottom of the screen Default values are loaded for Minimum Tanimoto Threshold and Maximum k value independent from the loaded SDF files e Enabling Preprocessing enables SymDex d versions of the algorithms to b
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