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LEIBNIZ-INSTITUT FÜR MOLEKULARE PHARMAKOLOGIEBERND RUPPChemical Information systems:From compound collections to rationall...
LEIBNIZ-INSTITUT FÜR MOLEKULARE PHARMAKOLOGIEThe Library Design TeamHead: Ronald KühneModule Cheminformatic/Drug DesignM. ...
LEIBNIZ-INSTITUT FÜR MOLEKULARE PHARMAKOLOGIEScreening Libraries @ FMP[CBB 6: - 1.280 Cpds, LOPAC-library ofpharmacologica...
LEIBNIZ-INSTITUT FÜR MOLEKULARE PHARMAKOLOGIEDatabase of Available Chemical Substances (DACS)Usage:- Experimental:design o...
LEIBNIZ-INSTITUT FÜR MOLEKULARE PHARMAKOLOGIEDACS 2005~20 vendors~ 2 million Cpds
LEIBNIZ-INSTITUT FÜR MOLEKULARE PHARMAKOLOGIEUpload History147 31112 489 62313 996 3504 350 90042 659 02205 000 00010 000 ...
LEIBNIZ-INSTITUT FÜR MOLEKULARE PHARMAKOLOGIEData Processing RoutineSD-FileSDBUDBFMP-DataManagementToolSD-FileWebinterface...
LEIBNIZ-INSTITUT FÜR MOLEKULARE PHARMAKOLOGIESD File collection 2012Vendor collection_count file_count mol_count Vendor co...
LEIBNIZ-INSTITUT FÜR MOLEKULARE PHARMAKOLOGIEDACS 20121101001 00010 000100 0001 000 00010 000 000100 000 000RecordsStruc...
LEIBNIZ-INSTITUT FÜR MOLEKULARE PHARMAKOLOGIESDB-RoutineSD-FileSDBUDBFMP-DataManagementToolSD-FileSDBWebinterfaceSearchtools
LEIBNIZ-INSTITUT FÜR MOLEKULARE PHARMAKOLOGIESD-File Registration- Determination of key data (Orderno., saltdata, vendor,f...
LEIBNIZ-INSTITUT FÜR MOLEKULARE PHARMAKOLOGIECatalog (SD-File) Registration
LEIBNIZ-INSTITUT FÜR MOLEKULARE PHARMAKOLOGIEImport Application Form
LEIBNIZ-INSTITUT FÜR MOLEKULARE PHARMAKOLOGIEImport controlling
LEIBNIZ-INSTITUT FÜR MOLEKULARE PHARMAKOLOGIEImport controlling
LEIBNIZ-INSTITUT FÜR MOLEKULARE PHARMAKOLOGIEER-Model of the SD-File RegistrationER-model := Entity relationship model
LEIBNIZ-INSTITUT FÜR MOLEKULARE PHARMAKOLOGIEUDB RoutineSD-FileSDBUDBFMP-DataManagementToolSDBUDBWebinterfaceSearchtools
LEIBNIZ-INSTITUT FÜR MOLEKULARE PHARMAKOLOGIEUnique structure database- Standardization of chemical Structures- Normalizat...
LEIBNIZ-INSTITUT FÜR MOLEKULARE PHARMAKOLOGIEER-Model of the UDB
LEIBNIZ-INSTITUT FÜR MOLEKULARE PHARMAKOLOGIESummarySDF-Registration 2007-2011: 99.2GBSDF-Registration 2012 : 116.7GBUDB 2...
LEIBNIZ-INSTITUT FÜR MOLEKULARE PHARMAKOLOGIEOutlook Web interface and start of the Webserver Implementation of FMP Reac...
LEIBNIZ-INSTITUT FÜR MOLEKULARE PHARMAKOLOGIEAcknowledgmentDrug Design / Molecular Modeling• Ronald Kühne, Dr.• Daniela Mü...
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EUGM 2013 - Bernd Rupp (FMP) Chemical Information systems: From compound collections to rationally designed HTS library

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The FMP has developed a database of commercially available compounds which is used to design our in-house HTS collection and is additionally applied to create focused libraries. But the dramatically increase of unique compounds of one order of magnitude from less than 10 to around 30 to 40 million compounds currently and approximately hundred million compounds in the next years requires a reorganization and redevelopment of our storage and searching strategy. To manage such a massive amount of data we developed a Registration Database for registration and normalisation of vendor catalogues. This database contains the highly redundant data of the vendor catalogues and is converted in a second step into the non-redundant Unique Structure Database which represents a data warehouse combining vendor data, structural descriptors and in-house classification tools including our earlier developed ADMET- and reactivity filters as well as our in-house fragment-based fingerprints used for library design tasks. The management of both database systems is part of a new developed Java application, which handles the user management for the data upload in the Registration Database and the conversion into the Unique Structure Database. Further a first version of a Web service is in preparation. This service allows the scientist not only to search for compounds and fragments in the Unique Structure Database but also to combine such a search with the FMP tools to classify compounds for their usability in biological assays.

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EUGM 2013 - Bernd Rupp (FMP) Chemical Information systems: From compound collections to rationally designed HTS library

  1. 1. LEIBNIZ-INSTITUT FÜR MOLEKULARE PHARMAKOLOGIEBERND RUPPChemical Information systems:From compound collections to rationallydesigned HTS library
  2. 2. LEIBNIZ-INSTITUT FÜR MOLEKULARE PHARMAKOLOGIEThe Library Design TeamHead: Ronald KühneModule Cheminformatic/Drug DesignM. Lisurek Design and enhancement ofScreening- Libraries Maintenance of Vendor-Data- Library Design: Design of focussed Libraries Design of Virtual Screens Design of Docking Studies Development of Homology Models- Modelling: Pharmacophore Models QSARModule Database Design and ITM. Pawletta, R. AL-Yamori and B. Rupp- Database design: Development and Maintenance of relationalDatabase of Screening results Development of commercial availablecompound library- Software development- Hardware Management Tools for Processing Structural Data
  3. 3. LEIBNIZ-INSTITUT FÜR MOLEKULARE PHARMAKOLOGIEScreening Libraries @ FMP[CBB 6: - 1.280 Cpds, LOPAC-library ofpharmacologically active annotated Cpds]2005 CBB 1: - 16.544 Cpds from ChemDiv2006/07 CBB 4: - 4.224 Cpds, ArtChem-libraryCBB 3: - 4.576 Cpds, fragment library2008/09 CBB 2: - 3.520 Cpds from Enamine, IBS,ChemDiv, KeyOrganics, Maybridge2011 CBB X: - 1.765 Cpds from IBS2012 CBB Y: - 2.600 Cpds from Enamineand UORSY[CBB 5: - 1.780 Cpds synthesized by academicgroups, collected by E. Specker]∑ ~35.000 Cpds€ 130.000€ ~10.000€ ~30.000€ ~80.000€ ~45.000€ ~45.000€ 20.000∑ € ~360.000
  4. 4. LEIBNIZ-INSTITUT FÜR MOLEKULARE PHARMAKOLOGIEDatabase of Available Chemical Substances (DACS)Usage:- Experimental:design of HTS, Ligation,Building Block und focusedLibraries- Theoretical:Virtual Screening, DockingTesting new MethodsAdvantages:- Effective Data Control- Individual Tagging and Searchfunctionality
  5. 5. LEIBNIZ-INSTITUT FÜR MOLEKULARE PHARMAKOLOGIEDACS 2005~20 vendors~ 2 million Cpds
  6. 6. LEIBNIZ-INSTITUT FÜR MOLEKULARE PHARMAKOLOGIEUpload History147 31112 489 62313 996 3504 350 90042 659 02205 000 00010 000 00015 000 00020 000 00025 000 00030 000 00035 000 00040 000 00045 000 0002006 2007 2008 2009 2010 2011 2012 2013Import YearRecordsStructures
  7. 7. LEIBNIZ-INSTITUT FÜR MOLEKULARE PHARMAKOLOGIEData Processing RoutineSD-FileSDBUDBFMP-DataManagementToolSD-FileWebinterfaceSearchtoolsVendor collectionsSD-File registrationUnique Structure
  8. 8. LEIBNIZ-INSTITUT FÜR MOLEKULARE PHARMAKOLOGIESD File collection 2012Vendor collection_count file_count mol_count Vendor collection_count file_count mol_countenamine 38 89 21.238.992,00 labotest 4 5 122.867,00ukrorgsynthesis 16 54 14.918.628,00 sigma_aldrich 3 4 118.392,00chemdiv 50 134 6.826.433,00 apollo_scientific 6 16 111.361,00aurora 9 31 5.494.875,00 zylexa 5 6 107.425,00vitas_m_lab 7 41 4.255.322,00 matrix_scientific 1 2 91.556,00otava 32 47 4.099.533,00 analyticon 5 15 84.037,00chembridge 20 41 4.038.934,00 nano_syn 2 9 65.327,00life_chemicals 76 95 2.875.379,00 toslab 9 15 47.944,00Ibs 4 24 1.908.031,00 arkad 1 1 31.102,00amri 9 18 1.258.137,00 fluorochem 1 1 29.304,00asinex 14 20 1.253.381,00 emc 1 1 28.932,00specs 16 19 1.140.632,00 asis_chem 19 19 24.485,00princeton_bio 12 15 949.659,00 peakdale 2 2 15.462,00timtec 11 21 535.435,00 spectrum_info 1 1 8.678,00pharmeks 2 5 524.224,00 evoblocks 1 1 8.367,00aronis 3 12 278.177,00 acb_blocks 3 3 6.561,00chemical_block 2 6 258.925,00 microsource 7 7 5.120,00nch_laboratories 3 3 230.831,00 sequoia 1 1 2.323,00ko_bionet 25 57 192.096,00 selleckchem 7 7 1.828,00arvi 2 58 180.728,00 combi_blocks 1 1 1.747,00maybridge 13 15 171.881,00 menai_organics_limited 1 3 652,00synthon_labs 3 3 129.544,00 Total: 43 448 928 73.673.247,00
  9. 9. LEIBNIZ-INSTITUT FÜR MOLEKULARE PHARMAKOLOGIEDACS 20121101001 00010 000100 0001 000 00010 000 000100 000 000RecordsStructuresUnique Structures
  10. 10. LEIBNIZ-INSTITUT FÜR MOLEKULARE PHARMAKOLOGIESDB-RoutineSD-FileSDBUDBFMP-DataManagementToolSD-FileSDBWebinterfaceSearchtools
  11. 11. LEIBNIZ-INSTITUT FÜR MOLEKULARE PHARMAKOLOGIESD-File Registration- Determination of key data (Orderno., saltdata, vendor,file, catalog, import_date, user...)- Testing of correct Syntax for Structure and Propertyblock- Upload into SD-File registration Database- Upload verification
  12. 12. LEIBNIZ-INSTITUT FÜR MOLEKULARE PHARMAKOLOGIECatalog (SD-File) Registration
  13. 13. LEIBNIZ-INSTITUT FÜR MOLEKULARE PHARMAKOLOGIEImport Application Form
  14. 14. LEIBNIZ-INSTITUT FÜR MOLEKULARE PHARMAKOLOGIEImport controlling
  15. 15. LEIBNIZ-INSTITUT FÜR MOLEKULARE PHARMAKOLOGIEImport controlling
  16. 16. LEIBNIZ-INSTITUT FÜR MOLEKULARE PHARMAKOLOGIEER-Model of the SD-File RegistrationER-model := Entity relationship model
  17. 17. LEIBNIZ-INSTITUT FÜR MOLEKULARE PHARMAKOLOGIEUDB RoutineSD-FileSDBUDBFMP-DataManagementToolSDBUDBWebinterfaceSearchtools
  18. 18. LEIBNIZ-INSTITUT FÜR MOLEKULARE PHARMAKOLOGIEUnique structure database- Standardization of chemical Structures- Normalization of the Data (removal ofredundancy)- Storage in a Data Warehouse system
  19. 19. LEIBNIZ-INSTITUT FÜR MOLEKULARE PHARMAKOLOGIEER-Model of the UDB
  20. 20. LEIBNIZ-INSTITUT FÜR MOLEKULARE PHARMAKOLOGIESummarySDF-Registration 2007-2011: 99.2GBSDF-Registration 2012 : 116.7GBUDB 2012 : 142.9GBMolecule Records: 73.64 MillStructure Records: 37.89 MillProperty Records: 65.72 MillSaltData Records: 2386Smallfragment Records: 4838Lost-molecule Records: 6360Duplicate Records: 2070Empty Records: 3582Error Records: 708Java 7 (jdk 1.7.10)Chemaxon 5.12MySQL 5.5.12 Missing files (42179 Records):error in count line of SD-File:Is fixed with jchem later than 5.12.33 2 0 0 0 0 0 0 03 2 0 0 0 0 0 0 0 0999 V2000Wrong count line:correct count line:
  21. 21. LEIBNIZ-INSTITUT FÜR MOLEKULARE PHARMAKOLOGIEOutlook Web interface and start of the Webserver Implementation of FMP Reactivityand Tox. Tag Implementation of FMP SolubilityPrediction and other in-house models Development of a GUI for UDB Routine Connection to other Public recourses likePubChem and ChEMBL Development of virtual Screening andDocking interfaces Update and Bug fix for SDF-Registrationand UDB-RoutineFurther Targets:Coming Soon:
  22. 22. LEIBNIZ-INSTITUT FÜR MOLEKULARE PHARMAKOLOGIEAcknowledgmentDrug Design / Molecular Modeling• Ronald Kühne, Dr.• Daniela Müller, Dr.• Kirill Piotukh, Dr.• Martyna Pawletta , master student• Raed Al-Yamori, tech. Informatics• Robert Opitz, Dr. student• Matthias Barone, Dr. student• Matthias Müller, Dr. student• Michael Lisurek, Dr.• Frank Eisenmenger, Dr.Screnning Unit/ CompoundManagment• Jens-Peter von Kries, Dr.• Martin Neuenschwander, Dr.• Edgar Specker, Dr.Former member:• Jörg Wichard, Dr. (Bayer AG)• Lara Kuhnke , master studentFunding:• Helmholtz Drug Researchinitiative; Ronald Frank, Dr.Partner:• Prof. Gerhard Wolber (FU Berlin)• Chemaxon

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