Agricultural Products Group 1 ChemAxons Marvin & JChem (v 3.1.3) vs. MDL® ISIS/Draw ISIS/Host (v...

1

Agricultural Products Group

ChemAxon’s Marvin & JChem (v 3.1.3)vs.

MDL® ISIS/Draw ISIS/Host (v 4.0)

Seong Jae Yu, David Roush, Usha GaneshYoung Moon, Henry Liu

2


• Business Discussion

• Scientific Evaluation

• Technical Evaluation

Outline

Comparison of MDL® ISIS/Host with JChem Base

3


Business Evaluation

• Customer Base

• Customer Support

• Cost/Benefit

4


Business Evaluation

• Customer Base


• Cost/Benefit

5


ChemAxon Clients

Industrial Clients: >200

Academic Clients: >900

For specific information: http://www.chemaxon.com/aboutus.html

6


Business Evaluation

• Customer Base

•Customer Support

• Cost/Benefit

7


Business Evaluation

• Customer Base


• Cost/Benefit

8


Scientific Evaluation

• DatabaseUsed 1.8 million compounds to create a testing database

• Searches 51 simple sub-structure searches 51 similarity searches

64 complex searchestautomers, double bond, stereochemistry, multiple substituents, valence, ring size, chain length, etc.

Total 115 structures were evaluated

9


Substructure Search Comparison (1)

NN

NO

O

N

NO

O

NONN

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

10



N

N

O

Single/aromatic

double

Query ChemAxon

43 hits 10 hits

Absent

N

N

O

double/aromatic

43 HitsNew Query

Change Bond Definition

S

N

NN

O

O

S

N

NN

O

O

N

N

N

NO

O

N

N

N

NO

O

MDL®

11



N

NO

O

single

Query ChemAxon

153 hits 146 hits

AbsentN

O

NO

R

SN N

NR

F FF

O

O

MDL®

12


Differences in MDL® Aromatic Definition

N

NO

O

single/aromatic

MDL® uses a precise definition for aromaticity of 6-membered rings

N

N

O

O

N

N

O

O

N

N

O

O

N

N

O

O

Ph

CN

N

NO

O

single

N

O

NO

R

SN

N

N

R

F FF

O

O

Query 2Query 1

MDL® uses a dual definition for aromaticity of 5-membered rings

13



Query ChemAxon

4959 hits 5020 hitsN

N N

N

N

N

N N

Absent

MDL®

14


NO

NO

O

NO

NO

O

NOT Lists

ChemAxon

1 hit 4 hits

Query

NO

NNOT [F,Cl,Br,I]

N

N

O

OO

H

N

NO

N

H

N

NO

OO

H

MDL®

15


Bidentate R groups

R

OH

ChemAxon

N/A hits 656 hits

MDL®

16


Atom Types

MDL® can not specify aromatic or aliphatic atoms

ChemAxon can specify aromatic or aliphatic atoms

O

ChemAxon Hits

Oa

OA

14

216

230

Query

Aromatic

Aliphatic

Aromatic/Aliphatic

17


Similarity Search Comparison (1)

N

NN

O

S

O

Query ChemAxon

0 hits(70%)

4 hits(75%)

ChemAxon Hits

N

NN

O N

S

OO N

N

O N

S

O N

N

N

S

O

O

N

O

N

NN

S

O

O

N

O

MDL®

18


NNO

Similarity Search Comparison (2)

Query ChemAxon

308 hits 302 hits

N

N

O

N

N

O

N

N

O

N

N

OO

NNO 1-3

MDL®

19


Overall Performance

BRIM_ID Substructure Similarity Substructure SimilarityBID-10007608 2.5 36.3 1 5BID-10055418 7.4 9.4 6 3BID-10622149 8.9 33.6 8 3BID-10699051 6.7 13.9 19 3BID-10978789 2.6 18.3 0 2BID-11192424 2.0 10.2 7 2BID-11252857 8.3 17.5 20 5BID-11706292 4.1 31.9 2 2BID-11800796 3.2 10.3 21 3BID-11885540 2.0 15.9 0 3

Average 4.8 19.7 8.4 3.1

MDL® (sec) Chemaxon (sec)

• Measure the performance (sec) based on 3 simultaneous users

20


ChemAxon – Product Overview

21


ChemAxon Standardizer

• Can remove counterions

• Aromaticity definition

• Structure standardization

22



• Can remove counterions• Aromaticity definition• Structure standardization

N NHCl

23



• MDL® treats 5-membered heterocycles as non-aromatic

(Kekulé structure)

• ChemAxon aromatizes any 4n+2 ring system

ISISKekulé structure

ChemAxonResonant structure

S S


24



5 hits in database 203 hits in database

NS

N

NS

N

NS

N


25




N+

O

O

NO

O

N

O

N+

O

25753 hitsin database

9 hitsin database

1105 hitsin database

92 hitsin database

26


Scientific Conclusion

• ChemAxon

- Is more logical and chemically meaningful in searches

- Can perform bidentate and atom-type searches

- Showed better search performance

- Can integrate other modules

- Flexible

• MDL®

- Can give unexpected results in similarity searches

- Databases (MDDR, ACD, REACCS)

27


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

28


1 Extract Ref #s per vendor 1 hr

2 Pipeline Pilot: split vendor files to {existing, discontinued, and new} per vendor

3 hr

3 Combine all the new files, filter, and generate unique/duplicate files 1 hr

4 Run the unique structures in a temp database in ISIS for uniqueness 1 hr

5 Remove duplicates from (4)

6 Export current ISIS 4 hr

7 Compare the unique file with export from (6) – generate unique and duplicate sdf

2 hr

8 Check if any of unique structures from (7) exists in ISIS 4 hr

9 If any from (8) remove from unique and duplicate files 1 hr

10

Assign compound ids to the new compounds 1 hr

11

Import into ISIS 2 hr

12

Create index 4 hr

13

Populate the Oracle master/detail tables 1 hr

14

Verify and Delete discontinued compounds 3 hrs

Testing at every stage 3 hrs

Total 31 hrs

Technical ComparisonExample of processing SD files in MDL® ISIS/Host

29


Technical ComparisonExample of processing SD files in ChemAxon

1 Populate filters in a table (Non-recurring)

7 hr2 Import vendor file into temporary table

3 Compare the vendor table to filter table and delete filtered

4 Run a procedure that insert new compounds into master/detail tables and flag discontinued.

5 (1-4) for all vendors

6 Create index on master table 0 hr

7 Verify dependencies and delete the compounds from detail table 4 hr

Total 11 hr

30


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

31


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

32


Summary: Business

ChemAxon was the better choice

33


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

34


Summary: Technical

• Clear and straightforward understanding of: Data Representation System Architecture

• Integrated system

Agricultural Products Group 1 ChemAxons Marvin & JChem (v 3.1.3) vs. MDL® ISIS/Draw ISIS/Host (v...

Documents

Transcript of Agricultural Products Group 1 ChemAxons Marvin & JChem (v 3.1.3) vs. MDL® ISIS/Draw ISIS/Host (v...