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Online chemical databasewith modeling environment”a summer school course
“
Sergii NovotarskyiIurii Sushko
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Chemoinformatics – overview of online resourcesChemical databases
1. PubChem — a database that provides information on the biologicalactivities of small molecules
2. ChemSpider — a free access service providing a structure centriccommunity for chemists
3. ChemIDplus — a tool, that provides chemical structure, property, andtoxicity searching
4. ChemBank — a database of chemical structures and assays
5. ChemDB — a set of chemoinformatics tools
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Chemoinformatics – overview of online resourcesLiterature databases
6. PubMed — a service, that includes over 19 million citations fromMEDLINE and other life science journals for biomedical articles back to1948
7. Toxicology Literature Online (TOXLINE) — references from toxicologyliterature
8. ScienceDirect — a full-text scientific database offering articles/chaptersfrom more than 2,500 peer-reviewed journals and more than 10,000books
9. ACS Publications — a worldwide scientific community with a collectionof the most cited peer-reviewed journals in the chemical and relatedsciences.
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Chemoinformatics – overview of online resourcesPubChem – start page
URL: http://pubchem.ncbi.nlm.nih.gov/ or for «PubChem»
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Chemoinformatics – overview of online resourcesPubChem – search results
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Chemoinformatics – overview of online resourcesPubChem – compound details
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Chemoinformatics – overview of online resourcesPubChem – bioassay search results
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Chemoinformatics – overview of online resourcesChemSpider – start page
URL: http://www.chemspider.com/ or for «ChemSpider»
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Chemoinformatics – overview of online resourcesChemSpider – search results
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Chemoinformatics – overview of online resourcesChemIdPlus – main page
URL: http://chem.sis.nlm.nih.gov/chemidplus/
for «ChemIdPlus»
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Chemoinformatics – overview of online resourcesChemIdPlus – search results
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Chemoinformatics – overview of online resourcesChemBank – main page
URL: http://chembank.broadinstitute.org/ or for «ChemBank»
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Chemoinformatics – overview of online resourcesChemBank – search results
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Chemoinformatics – overview of online resourcesChemDB – main page
URL: http://cdb.ics.uci.edu/ or for «ChemDB»
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Chemoinformatics – overview of online resourcesChemDB – search results
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Chemoinformatics – overview of online resourcesPubMed – main page
URL: http://www.ncbi.nlm.nih.gov/pubmed/ or for «PubMed»
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Online chemical database with modeling environmentThe subject of development
The web-based service
The database of physical, chemical and biological properties
Accumulating experimentally verified dataProviding user-friendly web-based access to this data
The QSPR modeling environment
Providing web-based tools for QSPR modelingStoring and “publishing” created models
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Online chemical database with modeling environmentMotivation
Our motivation
The importance of QSPR modeling
The importance of web-based tools for QSPR modeling
The importance to build one more service in this field
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Online chemical database with modeling environmentMotivation - QSPR
Structure-property relationship hypothesis:
QSPR modeling:
log (IC50) =0.64 log(µM)
log (IC50) =1.87 log(µM)
log (IC50) =1.87 log(µM)
log (IC50) = ?
“Similar structures - similar properties”
Predicting properties based on availabledata for structurally similar molecules.
Structures are represented by a set ofdescriptors (atom count, molecularweight).
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Online chemical database with modeling environmentQSPR – Similarity in descriptor space
Number of specific fragments in a molecule
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Online chemical database with modeling environmentMotivation - web-based tools for modeling
Main benefits of web-based tools:
Availability and accessibilityonly a computer with Internet access and a modern web-browser requiredto start working; possibility to share work materials among severallocations; works with any platform (Linux, Win, Mac)
Communication and collaborationpossibility to work on common topics, publish own results and use newresults of other people
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Online chemical database with modeling environmentMotivation - one more web-based tool
Reasons to build one more service:
Different approach to data modificationa completely open database, any user can add, delete and edit data (only
constrained by a set of simple rules)
Different approach to data organizationdata in the database is organized in a way, suitable for QSPR modeling
Integration of a database with modeling toolsdata from the database can be used for model creation and property
prediction
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Online chemical database with modeling environmentDistinctive features
The features, that make our service different:“Wiki” approach to data handlingusers can add, modify and delete data
Mandatory reference to an articleevery record in a database should contain a reference to an article, wherethe data was published
Storing additional informationwe store measurement conditions to increase data quality
Several tools to support decision makingintegration with other web-services (validation of molecule names againstPubChem database, automatic fetching of article information fromPubMed), duplicate records management
Aimed at model buildingconvenient to build training sets from data - filter by property, article andexport data either to internal modeling tools or download as Excel file
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Online chemical database with modeling environmentData structure
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Online chemical database with modeling environmentSimplified data structure
Records Properties
Molecules
ArticlesUnits
Journals
Conditions
Users
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Online chemical database with modeling environmentUser interface agreements
Browser-based interface
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Online chemical database with modeling environmentUser interface agreements
Browser-based interface
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Online chemical database with modeling environmentUser interface agreements
Icons
Edit current record (item, article, unit, etc.)
Delete current record
Most places — open record-specific submenu, sometimes — view profile
Open a wiki page with additional explanations
Send a message to the user
Download data in XLS format
Select item
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Online chemical database with modeling environmentSummary
The database currently contains:
More than 50000 records
Around 285 properties
More than 2700 articles
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Thank you
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Online chemical database with modeling environmentPractical course - outline
• Collection of data from original literature
• Use of publicly available tools for literature and cmemical structurelookup
• Introduction of data to OCHEM — single record
• Collection of data from benchmark literature
• Introduction of data to OCHEM — batch upload
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Online chemical database with modeling environmentPractical course – collection of data – before we start
Article name PubMedID Compound name Value
1
2
3
4
5
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Online chemical database with modeling environmentPractical course – collection of data
The goal: achive data on CYP450 1A2 inhibitors and noninhibitors
Cytochrome P450 (abbreviated CYP, P450, CYP450) is a very large and diversesuperfamily of hemoproteins found in all domains of life. © Wikipedia
PubMed search terms: CYP1A2 inhibition
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Online chemical database with modeling environmentPractical course – data collection
Article name PubMedID Compound name CYPModulation
1 Chemical genomics ofcancer chemopreventivedithiolethiones
19126641 •3H-1,2-dithiole-3-thione•4-methyl-5-pyrazinyl-3H-1,2-dithiole-3-thione•5-tert-butyl-3H-1,2-dithiole-3-thione
InhibitorNoninhibitorNoninhibitor
2 Comprehensive in vitroanalysis of voriconazoleinhibition of eight cytochromeP450 (CYP) enzymes: majoreffect on CYPs 2B6, 2C9,2C19, and 3A
19029318 Voriconazole Noninhibitor
3 Involvement of CYP1A2 inmexiletine metabolism 9690950 Mexiletine Inhibitor
4 Differential inhibition ofcytochrome P450 isoforms bythe protease inhibitors,ritonavir, saquinavir andindinavir
9278209 Indinavir Noninhibitor
5 An evaluation of potentialmechanism-based inactivationof human drug metabolizingcytochromes P450 bymonoamine oxidaseinhibitors,including isoniazid.
16669850 Clorgyline Inhibitor
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Online chemical database with modeling environmentPractical course – data introduction – cheat sheet
Good chemistry lookup engine: PubChem (find URL in Google.com)
We search by name, and want to get structure
Convenient structure representation - SMILES
Property: CYP450 Modulation
Condition: CYP450 Type = CYP1A2
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Online chemical database with modeling environmentPractical course – batch data introduction – template
• CASRN — CAS registration number• SMILES — smiles string• NAME — molecule name• ARTICLEID — article identifier (PubMed or OCHEM)• PAGE — article page• TABLE — article table• LINE — article line• COMMENT — text comment• REFERENCE — record reference• CYP450 Modulation — value of the property• Unit — measurment unit of the property• Accuracy — measurment accuracy• Interval — measurmen interval• CYP450 Type — record condition
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Online chemical database with modeling environmentPractical course – batch data introduction – cheat sheet
• Article URL: http://tinyurl.com/rendic• Article title: «Summary of information on human CYP enzymes:
human P450 metabolism data»• Good chemistry lookup engine: PubChem (find URL in Google.com)• We search by name, and want to get structure• Convenient structure representation - SMILES• Property: CYP450 Modulation• Condition: CYP450 Type = CYP1A2• Reference = 1• ArticleID = Q1592• Batch upload template URL: http://tinyurl.com/bu-template
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Thank you (once more)