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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) 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 • Customer Base • Customer Support • Cost/Benefit
Business Evaluation • Customer Base • Customer Support • Cost/Benefit
ChemAxon Clients Industrial Clients: 180 Academic Clients: >600 For specific information: http://www.chemaxon.com/aboutus.html
Business Evaluation • Customer Base • Customer Support • Cost/Benefit
Business Evaluation • Customer Base • Customer Support • Cost/Benefit
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
Complex Search (1) tautomers double bond stereochemistry
Complex Search (2) multiple substituents valence
Complex Search (3) ring size chain no substituent
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
Substructure Search Comparison (2) Query ChemAxon MDL® 43 hits 10 hits Absent New Query 43 Hits Change Bond Definition
Substructure Search Comparison (3) Query ChemAxon MDL® 153 hits 146 hits Absent
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
Substructure Search Comparison (3) MDL® Query ChemAxon 157 hits 155 hits Absent
Substructure Search Comparison (4) Query ChemAxon MDL® 4959 hits 5020 hits Absent
Substructure Search Comparison (5) MDL® Query ChemAxon 7810 hits 7810 hits 3622 hits 3622 hits
Substructure Search Comparison (6) MDL® Query ChemAxon 51906 hits 51906 hits 7015 hits 7015 hits
NOT Lists MDL® Query ChemAxon 1 hit 4 hits
Bidentate R groups MDL® ChemAxon N/A hits 656 hits
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
Similarity Search Comparison (1) Query ChemAxon MDL® 0 hits (70%) 4 hits (75%) ChemAxon Hits
Similarity Search Comparison (2) MDL® Query ChemAxon 308 hits 302 hits
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
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
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
ChemAxon Standardizer • Can remove counterions • Aromaticity definition • Structure standardization
ChemAxon Standardizer • Can remove counterions • Aromaticity definition • Structure standardization
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
ChemAxon Standardizer • Can remove counterions • Aromaticity definition • Structure standardization 5 hits in database 203 hits in database
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
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
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)
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
Technical Comparison Example of processing SD files in MDL® ISIS/Host
Technical Comparison Example of processing SD files in ChemAxon
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
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
Summary: Business ChemAxon was the better choice
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
Summary: Technical • Clear and straightforward understanding of: • Data Representation • System Architecture • Integrated system