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


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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
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

slide2

Outline

Comparison of MDL® ISIS/Host with JChem Base

  • Business Discussion
  • Scientific Evaluation
  • Technical Evaluation
business evaluation
Business Evaluation
  • Customer Base
  • Customer Support
  • Cost/Benefit
slide4

Business Evaluation

  • Customer Base
  • Customer Support
  • Cost/Benefit
chemaxon clients
ChemAxon Clients

Industrial Clients: 180

Academic Clients: >600

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

slide6

Business Evaluation

  • Customer Base
  • Customer Support
  • Cost/Benefit
slide7

Business Evaluation

  • Customer Base
  • Customer Support
  • Cost/Benefit
scientific evaluation
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
Complex Search (1)

tautomers

double bond

stereochemistry

complex search 2
Complex Search (2)

multiple substituents

valence

complex search 3
Complex Search (3)

ring size

chain

no substituent

substructure search comparison 1
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
Substructure Search Comparison (2)

Query

ChemAxon

MDL®

43 hits

10 hits

Absent

New Query

43 Hits

Change

Bond Definition

substructure search comparison 3
Substructure Search Comparison (3)

Query

ChemAxon

MDL®

153 hits

146 hits

Absent

differences in mdl aromatic definition
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 319
Substructure Search Comparison (3)

MDL®

Query

ChemAxon

157 hits

155 hits

Absent

substructure search comparison 4
Substructure Search Comparison (4)

Query

ChemAxon

MDL®

4959 hits

5020 hits

Absent

substructure search comparison 5
Substructure Search Comparison (5)

MDL®

Query

ChemAxon

7810 hits

7810 hits

3622 hits

3622 hits

substructure search comparison 6
Substructure Search Comparison (6)

MDL®

Query

ChemAxon

51906 hits

51906 hits

7015 hits

7015 hits

not lists
NOT Lists

MDL®

Query

ChemAxon

1 hit

4 hits

bidentate r groups
Bidentate R groups

MDL®

ChemAxon

N/A hits

656 hits

atom types
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
Similarity Search Comparison (1)

Query

ChemAxon

MDL®

0 hits

(70%)

4 hits

(75%)

ChemAxon Hits

similarity search comparison 2
Similarity Search Comparison (2)

MDL®

Query

ChemAxon

308 hits

302 hits

substructure search performance comparison
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
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
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
ChemAxon Standardizer
  • Can remove counterions
  • Aromaticity definition
  • Structure standardization
chemaxon standardizer33
ChemAxon Standardizer
  • Can remove counterions
  • Aromaticity definition
  • Structure standardization
chemaxon standardizer34
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 standardizer35
ChemAxon Standardizer
  • Can remove counterions
  • Aromaticity definition
  • Structure standardization

5 hits in database

203 hits in database

chemaxon standardizer36
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

calculator plugins
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
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)
slide39

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
slide40

Technical Comparison

Example of processing SD files in MDL® ISIS/Host

slide41

Technical Comparison

Example of processing SD files in ChemAxon

slide42

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
slide43

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
slide44

Summary: Business

ChemAxon was the better choice

slide45

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
slide46

Summary: Technical

  • Clear and straightforward understanding of:
    • Data Representation
    • System Architecture
  • Integrated system