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Structural Search Using ChemAxon Tools. Szabolcs Csepregi. JChem version 5.3, April 2010. Structural Search Using ChemAxon Tools. Interfaces Search types and options Query features , Stereo searching Special search types: reaction, R-group search, Chemical Terms filters

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structural search using chemaxon tools

Structural Search Using ChemAxon Tools

Szabolcs Csepregi

JChem version 5.3, April 2010

structural search using chemaxon tools1
Structural Search Using ChemAxon Tools


Search types and options

Query features, Stereo searching

Special search types: reaction, R-group search, Chemical Terms filters

Searching against Combinatorial Markush structures

Fingerprint screening


Applications of structural search:R-group decomposition, Standardizer,Reactor, Pmapper, Fragmenter

Future plans

All examples were generated by Marvin

structural search interfaces
Structural search interfaces
  • Example web GUI-s:
    • JSP(Java Server Pages)
    • AJAX example: Javascript and JChem Web Services
  • Command line: jcsearch
  • Java and .NET API:
    • MolSearchclass:in memory
    • JChemSearch class:in database
  • Cartridge: Oracle SQL
  • JChem Web Services
  • Instant JChem
  • JChem For Excel
search types in jchem
Search types in JChem

Structural search type



  • Atom By Atom Search or structural search:
  • Similarity search:
    • Different Descriptors
    • Different Metrics



Full structure


MC(E)S– maximum common (edge) substructure

s earch options

Some selected structure search options:

Stereo on/off/diastereomers

Ignore charge/isotope/radical/valence/polymers, etc.

Vague bond matching options

Chemical Terms filter

Tautomer search (even in substructure search)

Inverse hit list

Maximum search time / number of hits

Combine with non-structure conditions

Ordering of results

Similarity type / metric

Search options


query features 1 atomic features
Query features 1. Atomic features
  • Query atom types:
    • any(A, AH)
    • hetero (Q, QH)
    • list, not list
    • metal (M, MH)
    • halogen (X, XH)
    • periodic table groups (G1-18)
  • Pseudo atoms e.g. “Resin”
  • Explicit lone pairs (match to impliedlonepairs as well.)
  • Charge, isotope, radical
  • Link nodes (repeatable):
query features 3 atomic smarts features
Query features 3. Atomic SMARTS features
  • SMARTS atoms:
  • Additional query properties:
  • Example:
    • Carbonyl C, but not amide
query features 4 homology atoms
Query features 4. Homology atoms
  • Can be used:
    • In queries against molecule and reaction tables.
    • In Markush structures
  • Built-in and user-defined groups
query features 5 bond features components
Query features 5. Bond features & components
  • Query bond types: Any, single or double, single or aromatic, double or aromatic
  • Bond topology: chain/ring
  • Smarts bonds
  • Component level grouping
coordination compounds
Coordination compounds

Atom-to-atom (dative) and multicenter coordinate bonds.Alternative representations: Position variation bond

  • H representations:
    • Explicit
    • Implicit
    • Query H count:
      • total (H<n>)
      • implicit (h<n>)
  • Example:
stereo searching 1 double bonds





Cis or trans


Not trans

Not cis

Stereo searching 1. Double bonds
  • Levels of check:
    • All
    • Only marked double bonds (MDL: stereo care flag)
    • None
stereo searching 2 tetrahedral chirality



Up or down

Stereo searching 2. Tetrahedral chirality
  • Stereo bond types:
  • Relative stereo configuration
    • Chiral flag model
    • Enhanced stereo representation: AND<n>, OR<n>, ABS groups
groups integration query target
Groups integration (query & target)

Both sides are treated similarly by the search:

  • Abbreviations (super-atom S-groups):
  • Multiple groups:

Other S-groups supported: component, mixture, formulation , many polymer brackets:

reaction search
Reaction search
  • Reactants, agents, products
  • Transformation recognition (mapping)
  • Stereospecific reactions (inversion, retention)
  • Reactant grouping
  • Reacting center
r group search
R-group search
  • Scaffold, R-group definitions
  • Monovalent, divalent R-groups
  • R-logic
    • Occurrence
    • If-then
    • Rest H
undefined r atoms
Undefined R-atoms

- No substitution elsewhere


polymer storage and search
Polymer storage and search
  • Comprehensive representation
    • Source based and structure based
    • Copolymer types, mixtures, ladder-type polymers, etc
    • Phase shifting
    • End groups: specific, undefined, etc.
  • Flexible
    • Attached data search
    • Wide range of polymer search options
chemical terms filter
Chemical Terms filter
  • Chemically aware filtering for structure and similarity searches
  • Elements of the Chemical Terms language
    • structure matching functions (describing functional groups, reaction sites, similarity, etc)
    • property calculations (partial charge distribution, pKa, logP, HB donors, acceptors, topological descriptors, etc)
    • arithmetic and logic-operators
  • Examples
markush structures
Markush structures
  • Markush structure registration and search
  • Markush features
    • R-groups
    • Atom lists, bond lists
    • Position variation bond
    • Link nodes and repeating units
    • Homology groups
  • Compatible enumeration plugin
fingerprint screening in the database


JChem table



Hits for the query


Need to be searched

Atom by atom



Fingerprint screening in the database
  • JChem database searches use fingerprint technology for fastest search results.
  • It rapidly* filters out most non-hits -usually more than 99% of them are rejected.
  • Supported fingerprint types:
    • Chemical hashed fingerprints
    • User-defined additional structural keys

* Average screening time in a 3-million cached table: ~0.1s

application r group decomposition
Application: R-group decomposition

JChem is able to identify the ligands of a given scaffold at specified substitution positions:

Query(scaffold) Result




further applications of structural search in jchem
Further applications of structural search in JChem
  • Transformations - Standardizer & Reactor
  • Identification of pharmacophoric groups - Pmappernitro:amidine:
  • Identification of bond cleavage - Fragmenter

ether cut:

Enamine-amine tautomerism:

Converting covalent form of alcoholates to ionic form:


Substructure searching in 19.5 million structures (Pubchem) JChem Base 5.2.2, Intel Quad Q6600 2.4GHz, 8 GB RAM; Oracle

Compound registration:

future plans
Future plans
  • R-group decomposition GUI in client applications
  • Visualization of similarity search results using MCS
  • Diastereomer search
  • Markush search enhancements (homology variation conditions, maximum common substructure, etc)
  • JChem suite: contains a broad range of chemical search facilities, including Markush structure analysis.
  • Structural search is a useful tool for many applications.
  • JChem Query Guide
  • Chemical Terms reference
  • JChem Base JSP demo page
  • Jcsearch command line tool
  • API documentation
  • (, chemaxon.jchem.db.JChemSearch)
  • JChem Base
  • JChem Cartridge
  • Instant JChem
  • JChem for Excel
thank you for your attention
Thank you for your attention

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