Agricultural Products Group 1 ChemAxons 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

Agricultural Products Group 2 Business Discussion Scientific Evaluation Technical Evaluation Outline Comparison of MDL® ISIS/Host with JChem Base

Agricultural Products Group 3 Business Evaluation Customer Base Customer Support Cost/Benefit

Agricultural Products Group 4 Business Evaluation Customer Base Customer Support Cost/Benefit

Agricultural Products Group 5 ChemAxon Clients Industrial Clients: 180 Academic Clients: >600 For specific information:

Agricultural Products Group 6 Business Evaluation Customer Base Customer Support Cost/Benefit

Agricultural Products Group 7 Business Evaluation Customer Base Customer Support Cost/Benefit

Agricultural Products Group 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

Agricultural Products Group 9 Scaffold Search (1)

Agricultural Products Group 10 Scaffold Search (2)

Agricultural Products Group 11 Scaffold Search (3)

Agricultural Products Group 12 Complex Search (1) tautomers double bond stereochemistry

Agricultural Products Group 13 Complex Search (2) multiple substituents valence

Agricultural Products Group 14 Complex Search (3) ring size chain no substituent

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

Agricultural Products Group 16 Substructure Search Comparison (2) QueryChemAxon 43 hits10 hits Absent 43 HitsNew Query Change Bond Definition MDL®

Agricultural Products Group 17 Substructure Search Comparison (3) QueryChemAxon 153 hits146 hits Absent MDL®

Agricultural Products Group 18 Substructure Search Comparison (3)

Agricultural Products Group 19 Differences in MDL® Aromatic Definition MDL® uses a precise definition for aromaticity of 6-membered rings Query 2Query 1 MDL® uses a dual definition for aromaticity of 5-membered rings

Agricultural Products Group 20 Substructure Search Comparison (3) ChemAxonQuery 157 hits155 hits Absent MDL®

Agricultural Products Group 21 Substructure Search Comparison (4) QueryChemAxon 4959 hits5020 hits Absent MDL®

Agricultural Products Group 22 Substructure Search Comparison (5) QueryChemAxon 7810 hits 3622 hits MDL®

Agricultural Products Group 23 Substructure Search Comparison (6) QueryChemAxon hits 7015 hits MDL®

Agricultural Products Group 24 NOT Lists ChemAxon 1 hit4 hits QueryMDL®

Agricultural Products Group 25 Bidentate R groups ChemAxon N/A hits656 hits MDL®

Agricultural Products Group 26 Atom Types MDL® can not specify aromatic or aliphatic atoms ChemAxon can specify aromatic or aliphatic atoms ChemAxon Hits Query Aromatic Aliphatic Aromatic/ Aliphatic

Agricultural Products Group 27 Similarity Search Comparison (1) QueryChemAxon 0 hits (70%) 4 hits (75%) ChemAxon Hits MDL®

Agricultural Products Group 28 Similarity Search Comparison (2) QueryChemAxon 308 hits302 hits MDL®

Agricultural Products Group 29 Substructure Search Performance Comparison QueryMDL®ChemAxon HitsTime(s)HitsTime(s)

Agricultural Products Group 30 Similarity Search Performance Comparison QueryChemAxon 213 HitsTime(s)HitsTime(s) MDL®

Agricultural Products Group 31 Complex Search Performance Comparison QueryChemAxon 333 HitsTime(s)HitsTime(s) MDL®

Agricultural Products Group 32 Overall Performance Measure the performance (sec) based on 3 simultaneous users

Agricultural Products Group 33 ChemAxon – Product Overview

Agricultural Products Group 34 ChemAxon Standardizer Can remove counterions Aromaticity definition Structure standardization

Agricultural Products Group 35 ChemAxon Standardizer Can remove counterions Aromaticity definition Structure standardization

Agricultural Products Group 36 ChemAxon Standardizer MDL® treats 5-membered heterocycles as non-aromatic (Kekulé structure) ChemAxon aromatizes any 4n+2 ring system ISIS Kekulé structure ChemAxon Resonant structure Can remove counterions Aromaticity definition Structure standardization

Agricultural Products Group 37 Can remove counterions Aromaticity definition Structure standardization 5 hits in database 203 hits in database ChemAxon Standardizer

Agricultural Products Group 38 ChemAxon Standardizer Can remove counterions Aromaticity definition Structure standardization hits in database 9 hits in database 1105 hits in database 92 hits in database

Agricultural Products Group 39 Calculator Plugins Available Calculations Elemental analysis Charge distribution Polarizability pK a logP logD Major microspecies Polar surface area Hückel Analysis H-bond donor-acceptor Refractivity Calculation Interface Marvin GUI Command line API

Agricultural Products Group 40 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)

Agricultural Products Group 41 Technical Comparison Transparency Proprietary (opaque) data/table structure Clear understanding of: Flow of Data Structure of Data Execution Process SDFile Processing Lack of necessary tools to process large SDFiles Requires several custom programs Simple SDFile processing and manipulation ISIS ChemAxon ISIS ChemAxon

Agricultural Products Group 42 1Extract Ref #s per vendor1 hr 2Pipeline Pilot: split vendor files to {existing, discontinued, and new} per vendor3 hr 3Combine all the new files, filter, and generate unique/duplicate files1 hr 4Run the unique structures in a temp database in ISIS for uniqueness1 hr 5Remove duplicates from (4) 6Export current ISIS4 hr 7Compare the unique file with export from (6) – generate unique and duplicate sdf2 hr 8Check if any of unique structures from (7) exists in ISIS4 hr 9If any from (8) remove from unique and duplicate files1 hr 10Assign compound ids to the new compounds1 hr 11Import into ISIS2 hr 12Create index4 hr 13Populate the Oracle master/detail tables1 hr 14Verify and Delete discontinued compounds3 hrs Testing at every stage3 hrs Total31 hrs Technical Comparison Example of processing SD files in MDL® ISIS/Host

Agricultural Products Group 43 Technical Comparison Example of processing SD files in ChemAxon 1Populate filters in a table (Non-recurring) 7 hr 2Import vendor file into temporary table 3Compare the vendor table to filter table and delete filtered 4Run a procedure that insert new compounds into master/detail tables and flag discontinued. 5(1-4) for all vendors 6Create index on master table0 hr 7Verify dependencies and delete the compounds from detail table4 hr Total11 hr

Agricultural Products Group 44 Supported Platforms ISIS® : Sun Solaris®, Windows® Servers JChem:Sun Solaris®, Windows® Servers, Linux®, Irix®, MAC® Technical Comparison Technologic Transparency ISIS®:Unclear Data/Table Structures JChem:Clear Understanding of: Flow of Data Structure of Data Execution Process Native Oracle Tables and Procedures Processing SD Files ISIS®:31 hours, Pipeline® Pilot & ISIS® JChem:11 hours, JChem Supported Databases ISIS®:Oracle® JChem:Oracle®, MySQL®, SQL Server, PostgreSQL, Access, DB2 Performance ISIS®:Slow similarity search JChem:Fast similarity search

Agricultural Products Group 45 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

Agricultural Products Group 46 Summary: Business ChemAxon was the better choice

Agricultural Products Group 47 Major Differences: result from aromatic bond definitions 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 Summary: Scientific Not List includes only your choices with ChemAxon Bidentate searches and atom types possible in ChemAxon MDL® has MDDR, ACD and REACCS databases

Agricultural Products Group 48 Summary: Technical Clear and straightforward understanding of: Data Representation System Architecture Integrated system