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ChemAxon’s Marvin & JChem (v 3.1.3) vs. MDL® ISIS/Draw ISIS/Host (v 4.0)

ChemAxon’s Marvin & JChem (v 3.1.3) vs. MDL® ISIS/Draw ISIS/Host (v 4.0). Seong Jae Yu, David Roush, Usha Ganesh Young Moon, Henry Liu. Outline Comparison of MDL ® ISIS/Host with JChem Base. Business Discussion Scientific Evaluation Technical Evaluation. Business Evaluation.

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ChemAxon’s Marvin & JChem (v 3.1.3) vs. MDL® ISIS/Draw ISIS/Host (v 4.0)

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  1. ChemAxon’s Marvin & JChem (v 3.1.3)vs. MDL® ISIS/Draw ISIS/Host (v 4.0) Seong Jae Yu, David Roush, Usha Ganesh Young Moon, Henry Liu

  2. Outline Comparison of MDL® ISIS/Host with JChem Base • Business Discussion • Scientific Evaluation • Technical Evaluation

  3. Business Evaluation • Customer Base • Customer Support • Cost/Benefit

  4. Business Evaluation • Customer Base • Customer Support • Cost/Benefit

  5. ChemAxon Clients Industrial Clients: 180 Academic Clients: >600 For specific information: http://www.chemaxon.com/aboutus.html

  6. Business Evaluation • Customer Base • Customer Support • Cost/Benefit

  7. Business Evaluation • Customer Base • Customer Support • Cost/Benefit

  8. Scientific Evaluation • Database • Used 1.8 million compounds to create a testing database • Searches • 51 simple sub-structure searches • 51 similarity searches • 64 complex searches • tautomers, double bond, stereochemistry, multiple substituents, valence, ring size, chain length, etc. • Total 115 structures were evaluated

  9. Scaffold Search (1)

  10. Scaffold Search (2)

  11. Scaffold Search (3)

  12. Complex Search (1) tautomers double bond stereochemistry

  13. Complex Search (2) multiple substituents valence

  14. Complex Search (3) ring size chain no substituent

  15. Substructure Search Comparison (1) 25 out of 51 searches showed identical results MDL® ChemAxon Query 3 hits 3 hits 79 hits 79 hits 5545 hits 5545 hits 6087 hits 6087 hits

  16. Substructure Search Comparison (2) Query ChemAxon MDL® 43 hits 10 hits Absent New Query 43 Hits Change Bond Definition

  17. Substructure Search Comparison (3) Query ChemAxon MDL® 153 hits 146 hits Absent

  18. Differences in MDL® Aromatic Definition Query 1 Query 2 MDL® uses a dual definition for aromaticity of 5-membered rings MDL® uses a precise definition for aromaticity of 6-membered rings

  19. Substructure Search Comparison (3) MDL® Query ChemAxon 157 hits 155 hits Absent

  20. Substructure Search Comparison (4) Query ChemAxon MDL® 4959 hits 5020 hits Absent

  21. Substructure Search Comparison (5) MDL® Query ChemAxon 7810 hits 7810 hits 3622 hits 3622 hits

  22. Substructure Search Comparison (6) MDL® Query ChemAxon 51906 hits 51906 hits 7015 hits 7015 hits

  23. NOT Lists MDL® Query ChemAxon 1 hit 4 hits

  24. Bidentate R groups MDL® ChemAxon N/A hits 656 hits

  25. Atom Types MDL® can not specify aromatic or aliphatic atoms ChemAxon can specify aromatic or aliphatic atoms Query ChemAxon Hits Aromatic 14 Aliphatic 216 Aromatic/ Aliphatic 230

  26. Similarity Search Comparison (1) Query ChemAxon MDL® 0 hits (70%) 4 hits (75%) ChemAxon Hits

  27. Similarity Search Comparison (2) MDL® Query ChemAxon 308 hits 302 hits

  28. Substructure Search Performance Comparison Query MDL® ChemAxon Hits Time(s) Hits Time(s) 5545 16 5545 13 287 4 287 3 99 2 99 0 110 3 110 0

  29. Similarity Search Performance Comparison Query ChemAxon MDL® Hits Time(s) Hits Time(s) 3 21 3 2 106 15 201 1 138 29 151 1 308 47 302 2

  30. Complex Search Performance Comparison Query MDL® ChemAxon Hits Time(s) Hits Time(s) 33 3 33 3 2516 13 2516 120 11 3 11 8 627 2 627 1

  31. ChemAxon – Product Overview

  32. ChemAxon Standardizer • Can remove counterions • Aromaticity definition • Structure standardization

  33. ChemAxon Standardizer • Can remove counterions • Aromaticity definition • Structure standardization

  34. ChemAxon Standardizer • Can remove counterions • Aromaticity definition • Structure standardization • MDL® treats 5-membered heterocycles as non-aromatic • (Kekulé structure) • ChemAxon aromatizes any 4n+2 ring system ISIS Kekulé structure ChemAxon Resonant structure

  35. ChemAxon Standardizer • Can remove counterions • Aromaticity definition • Structure standardization 5 hits in database 203 hits in database

  36. ChemAxon Standardizer • Can remove counterions • Aromaticity definition • Structure standardization 25753 hits in database 9 hits in database 1105 hits in database 92 hits in database

  37. Available Calculations Elemental analysis Charge distribution Polarizability pKa logP logD Major microspecies Polar surface area Hückel Analysis H-bond donor-acceptor Refractivity Calculation Interface Marvin GUI Command line API Calculator Plugins

  38. Scientific Conclusion • ChemAxon • - Is more logical and chemically meaningful in searches • - Can perform bidentate searches • - Showed better search performance • - Can integrate other modules • - Flexible • MDL® • - Can give unexpected results in similarity searches • - Databases (MDDR, ACD, REACCS)

  39. Technical Comparison Transparency ISIS ChemAxon • Proprietary (opaque) data/table structure • Clear understanding of: • Flow of Data • Structure of Data • Execution Process SDFile Processing ISIS ChemAxon • Lack of necessary tools to process large SDFiles • Requires several custom programs • Simple SDFile processing and manipulation

  40. Technical Comparison Example of processing SD files in MDL® ISIS/Host

  41. Technical Comparison Example of processing SD files in ChemAxon

  42. Technical Comparison • Supported Platforms • ISIS®: Sun Solaris®, Windows® Servers • JChem: Sun Solaris®, Windows® Servers, Linux®, Irix®, MAC® • Supported Databases • ISIS®: Oracle® • JChem: Oracle®, MySQL®, SQL Server, PostgreSQL, Access™, DB2 • Processing SD Files • ISIS®: 31 hours, Pipeline® Pilot & ISIS® • JChem: 11 hours, JChem • Technologic Transparency • ISIS®: Unclear Data/Table Structures • JChem: Clear Understanding of: • Flow of Data • Structure of Data • Execution Process • Native Oracle Tables and Procedures • Performance • ISIS®: Slow similarity search • JChem: Fast similarity search

  43. Technical Conclusion • Clear and straightforward understanding of • Data Representation • System Architecture • Integrated system • Quicker and less error-prone • Less hassle for software development • From technical point of view, ChemAxon is favorable

  44. Summary: Business ChemAxon was the better choice

  45. Summary: Scientific • Used 1.8 million vendor compounds to create a testing database • Prepared 115 different structures for comparison • 51 simple sub-structure search • 51 similarity search • 64 complex search Major Differences: result from aromatic bond definitions • Not List includes only your choices with ChemAxon • Bidentate searches and atom types possible in ChemAxon • MDL® has MDDR, ACD and REACCS databases

  46. Summary: Technical • Clear and straightforward understanding of: • Data Representation • System Architecture • Integrated system

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