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MultiMCS: A Fast Algorithm for the Maximum Common Substructure Problem on Multiple Molecules Publication
Several efficient correspondence graph-based algorithms for determining the maximum common substructure (MCS) of a pair of molecules have been published in the literature. The extension o…
March 2011
Using Consensus-Shape Clustering To Identify Promiscuous Ligands and Protein Targets and To Choose the Right Query for Shape-Based Virtual Screening Publication
Ligand-based shape matching approaches have become established as important and popular virtual screening (VS) techniques. However, despite their relative success, many authors have discu…
May 2011
Product group:
Discovery toolkit
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
Discovery of Chemical Compound Groups with Common Structures by a Network Analysis Approach (Affinity Prediction Method) Publication
We developed a method in which the relationship between chemical compounds, characterized by the secondary dimensional descriptors by a standard method, is first determined by network inf…
January 2011
Product group:
Discovery toolkit
'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…
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
Clustering studies on 5-HT4 ligands Poster
5-HT4 receptors are implied in various peripheral and central functions, such as gastro-intestinal tonicity and secretions, as well as the modulation of emotional behaviour and cognitive …
June 2007
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
Comparison of Three Preprocessing Filters Efficiency in Virtual Screening: Identification of New Putative LXR? Regulators As a Test Case Publication
In silico screening methodologies are widely recognized as efficient approaches in early steps of drug discovery. However, in the virtual high-throughput screening (VHTS) context, where h…
April 2010
Product group:
Discovery toolkit
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
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
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
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
Clustering for the Masses: Pairing JKlustor with Seurat Presentation
This presentation will discuss the integration of ChemAxon’s JKlustor with Synaptic Science’s Seurat to provide easy-to-use substructure clustering capabilities to biologists …
August 2008
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 …
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
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