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Finding Key Members in Compound Libraries by Analyzing Networks of Molecules Assembled by Structural Similarity Publication
Characterization of chemical libraries is an essential task in everyday chemoinformatics practice. This study describes some potential uses of network visualization and analysis methods t…
October 2009
Virtual Libraries and Virtual Screening in Drug Discovery Processes using KNIME Presentation
Based around ChemAxon’s discovery tools we will discuss key aspects of virtual high throughput screening methods including management and characterization of virtual libraries, alte…
The New JKlustor Suite Presentation
JKlustor, ChemAxon’s first package providing capabilities beyond core cheminformatics has been intensively developed in the past few years. Diverse problems ranging form the crude …
September 2009
'Natural' Clustering: An approximate MCES algorithm used on WOMBAT Presentation
We describe a clustering procedure for chemical compounds, which can rapidly be deployed on large compound libraries. The procedure creates initial cluster seeds starting from fingerprint…
Structure Based Clustering of NCI's Anti-HIV Library Poster
To support clustering, new software called JKlustor has been developed as an add-on module for ChemAxon’s chemical database handling system, JChem. The application can generate 2D h…
July 2001
Product group:
Discovery toolkit
Maximum Common Substructure Based Hierarchical Clustering Poster
Clustering chemical structures is a widely used method in various phases of the drug discovery process. Possible applications range from clustering virtual hit sets consisting of 1000’s…
June 2008
Product group:
Discovery toolkit
HSP90 Ligands Chemical Diversity of Known Molecules and Discovery of New Potential Hits by Virtual Screening Presentation
Hsp90 has emerged as a promising target for new cancer therapeutics, with the perspective of simultaneous disruption of a large range of oncogenic pathways. HSP 90 Inhibitors could result…
May 2008
Clustering made human Presentation
Clustering chemical structures alleviates the tedious task of browsing a large set of compounds by grouping individual structures into generic categories. ChemAxon’s JKlustor produc…
The New JKlustor Suite Presentation
JKlustor, ChemAxon’s first package providing capabilities beyond the core cheminformatics, offers versatile clustering techniques. Diverse problems ranging form crude clustering of …
June 2009
Product group:
Discovery toolkit
Using ChemAxon tools in Accamba, a project for modelling screening results based on machine learning methods Poster
The Accamba project (
June 2006
JKlustor - latest with library MCS Presentation
Recent advances in maximum common substructure (MCS) based clustering is overviewed in this presentation. Special attention is paid to the accomplishment of the development roadmap presen…
June 2007
Improved Virtual Screening Strategies and Enrichment of Focused Libraries in Active Compounds Using Target-Oriented Databases Presentation
Aureus Pharma has constituted and maintains a unique and comprehensive database regrouping all the data already published on GPCR and Ion channel medicinal chemistry and pharmacology. Che…
Drug Discovery in the sandbox Presentation
Four scientists muddy their paws in early phase drug discovery. Bravely our heroes apply ChemAxon’s discovery tools in their challenge. Will they succeed? Will you? All-star toolkit…
September 2010
Product group:
Discovery toolkit
Maximum Common Substructure Based Hierarchical Clustering Poster
Clustering chemical structures is a widely used method in various phases of the drug discovery process. Possible applications range from clustering virtual hit sets consisting of 1000’s…
August 2008
Product group:
Discovery toolkit
Chemoinformatics: Theory, Practice and Products; Chapter 2.7 Publication
Product overview in the Chapter 2.7 of the Chemoinformatics: Theory, Practice and Products book, Page 87.
January 2007
Maximum Common Substructure Based Hierarchical Clustering Poster
Clustering chemical structures is a widely used method in various phases of the drug discovery process. Possible applications range from clustering virtual hit sets consisting of 1000’s…
September 2006
Product group:
Discovery toolkit
Drug- and Lead-likeness, Target Class, and Molecular Diversity Analysis of 7.9 Million Commercially Available Organic Compounds Provided by 29 Suppliers Publication
A database of 7.9 million compounds commercially available from 29 suppliers in 2008−2009 was assembled and analyzed. 5.2 million structures of this database were identified to be uniqu…
March 2010
Clustering Files of Chemical Structures Using the Székely-Rizzo Generalisation of Ward’s Method Publication
Ward’s method is extensively used for clustering chemical structures represented by 2D fingerprints. This paper compares Ward clusterings of 14 datasets (containing between 278 and …
JKlustor Presentation
March 2010
Product group:
Discovery toolkit
Compound library annotation Presentation
Key Topics:
Virtual screening
Molecular descriptors
Pharmacophore similarity
Chemical space
Clustering
Scaffold
Maximum Common Substructure
Total diversity
Additional resources
Recent s…
Maximum Common Substructure Presentation
Preliminary topics
1. Theory
- MCS, MCES, MOS, complexity
- approaches to find MCS
- ChemAxon’s approach, comparison
2. MCS based clustering
- why
- problems
- how, speed issues, …
June 2006
What's new in JKlustor, LibMCS Presentation
his workshop discusses the novel clustering technique, the maximum common substructure (MCS) based hierarchical clustering available in the JKlustor tool.
The concept of the MCS and its …
June 2006
Product group:
Discovery toolkit
Clustering with JKlustor Tutorial
To try our clustering tools please visit the
April 2010
Product group:
Discovery toolkit
Library MCS demo animation Tutorial
November 2009
Product group:
Discovery toolkit
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