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EUGM 2013 - Roland Knispel (ChemAxon) - Biologics at ChemAxon From Old Powerhouses to Novel Tools
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EUGM 2013 - Roland Knispel (ChemAxon) - Biologics at ChemAxon From Old Powerhouses to Novel Tools

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Biologics have become an integral part of the drug development cycle within the pharmaceutical industry. But current cheminformatics toolkits are not well-suited to facilitate representation and …

Biologics have become an integral part of the drug development cycle within the pharmaceutical industry. But current cheminformatics toolkits are not well-suited to facilitate representation and computational interrogation of large biomolecules in the same way as for small molecules. Our Marvin suite is the product most frequently exposed to our users, and with recent releases, we aimed to continuously improve support for its application in a biopharmaceutical setting. But where these improvements are a mere extension of our classical cheminformatics tools, we have taken up development of a novel Biomolecule toolkit in parallel. It shall address the identified shortcomings in the data handling of large biomolecules with full atomic description, comparison of large biomolecules, and the exposure of distinct data views for different specialty groups of scientists. In this short presentation we will outline our future roadmap in the biological sector.

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  • 1. Biologics - From old powerhousesto novel toolsRoland Knispel
  • 2. * Inside BIO Industry Analysis, David Thomas, CFA, 01/17/201328/39 new therapeutics approved by FDA weresmall molecule drugsNew drug approvals in 2012*30% of new therapeutics approved by FDA wereBiologics
  • 3. FASTA importBiologics in MarvinSketch 6.0
  • 4. Unlimited attachment points for S-groupsBiologics in MarvinSketch 6.01-Phospho-histidine3-Phospho-histidine43
  • 5. • Sequence bridges, cyclizations• Leaving groupsIn progress
  • 6. • Improved clean-up upon sequence residueexpansionIn progress
  • 7. New tools for information management
  • 8. At the heart ofCorporate Business IntelligenceChemAxon Registration solutionRegistrationWeb ServicesWeb ClientsChemist Biologist AdministratorsProject LeaderELN FeederBulk LoaderData ProviderInterfacesDownstreamApplicationsDownstreamData StoresUser groupsFeeder systems Consumer systemsRegistrar
  • 9. • Distinct descriptors of biological entities• Lack of representation standards• Highly dynamic R&D workflows• Genealogy-dependent uniquenessBiologics registration challengesS126
  • 10. • Integrated browser-based registration system– Agnostic data model– Mapping of workflow processes to business logic• Data mart capabilities• BioSketcher• Webservice-based architectureLong-term goals
  • 11. • Java-based toolkit and webservices facilitating– Standardization and canonicalization ofBio-macromolecule representation– DB storage and simple queries– Duplicate checks– Full HELM notation support• HELM editor applet as early stage GUIShort-term goals
  • 12. • Externalized fromPfizer for PistoiaAlliance project• Established tools inBiotherapeuticalsR&D at PfizerHELM editor and notation toolkit
  • 13. Example – HELM notationRNA1{R(A)P.R(G)P.R(C)PS.R(U)}|PEPTIDE1{K.K.K.G.C}|CHEM1{PEG3}$RNA1,CHEM1,16:R2-1:R1|PEPTIDE1,CHEM1,5:R2-1:R2$$RNA1{StrandType:ss}$Definitions of simple polymersConnectivity of simple polymersAnnotation tagsNotationStructureRNA1CHEM1PEPTIDE1Bond[16:R2-1:R1]Bond[5:R2-1:R2]x
  • 14. Stage 1: Bio-molecule toolkitAPIBiomolecule DBHELM Notation ToolkitHELM parserStandardization/CanonicalizationDuplicate checkWebservice CoreHELMHELMBrowserapplicationFeeder serviceHELM Editor*** As part of Pistoia Alliance HELM project, based on Pfizer tools
  • 15. Stage 2: Bio-molecule toolkitAuxiliayWebservicesSequence BLASTCalculatorsCoordinate mappingCompReg Link ServiceAPIBiomolecule DBHELM Notation ToolkitHELM parserStandardization/CanonicalizationDuplicate checkWebservice CoreHELMHELMBrowserapplicationFeeder serviceHELM Editor*** As part of Pistoia Alliance HELM project, based on Pfizer tools
  • 16. IJC integrationBioCore APIJChem tablesfor BiologicsID Structure Formula Length MW EC1C130H190N32O41S228 2921 171902C155H238N44O46S130 3486 126603C121H196N38O3525 2743 5690
  • 17. – Full HELM support– SOAP/REST-supporting Core and DAO webservicesfor Bio-molecule registration DB– Limited performance constraintsOption for interested parties to– Evaluate features and integration capabilities– Engage in joint discussions for future developmentsToolkit alpha version in Summer 2013
  • 18. Stay tuned...Q3Q4Q1Q2Bio-molecule toolkitAlpha version*Bio-molecule registrationBio-material registration20132014* Contact us to find out moreModularRegistrationSystem