Author: Ferenc Csizmadia

JChem: Java Applets and Modules Supporting Chemical Database Handling from Web Browsers

Jan 25, 2000 - Publication
A Java based development tool for building portable chemical information systems is presented. The system contains applets for constructing web-based interfaces and classes that add struc…
Product: JChem Base

Making “Real” Molecules in Virtual Space

Jan 13, 2006 - Publication
Predicting “realistic” compounds of given chemical reactions with virtual synthesis tools usually requires the manual intervention of experienced chemists in the enumeration p…
tautomer

Tautomer generation. pKa based dominance conditions for generating dominant tautomers

Aug 23, 2007 - Poster
The ChemAxon added a new Calculator Plugin to the Marvin and JChem product families in 2007 to generate the tautomeric structures of a molecule. The new functionalities offer a wide range…
donor

Virtual Screening Using Fingerprints Part I. A Hybrid Approach to Pharmacophore Point Perception

Aug 15, 2003 - Poster
About 90% of drug targets cannot be crystallized. If the 3D structure of the active site is not available, a pharmacophore model is created. Such models are typically based on compounds t…
novel

A Novel Approach to Modeling Molecular Transformations and its Various Applications

Aug 15, 2003 - Poster
With the advent of high throughput screening and combinatorial chemistry computer assisted chemistry plays an important role in selecting and designing new drug candidates. Pharmaceutical…

Latest Developments in Markush Representation, Search, Analysis and Visualization

Mar 14, 2012 - Poster
Scientific poster at the International Patent Information Conference and Exposition (IPI-ConfEx) Markush structures are widely used in patent claims to maximize intellectual property pro…
jklustor

Maximum Common Substructure Based Hierarchical Clustering

Sep 14, 2006 - 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…
cartarchitecture

JChem Cartridge: Cheminformatics Platform for Oracle

Mar 16, 2006 - Poster
JChem Cartridge adds chemical knowledge to the Oracle platform. Data can be searched by structure, substructure and similarity criteria through extending Oracle’s native SQL languag…
virtualsynthesis

Virtual synthesis with “smart” reactions

Nov 15, 2003 - Poster
Modeling chemical structures is a scientifically well grounded area, proving it’s self in theory as well as in practice. However, there are many traps on the road to virtual reaction pr…
standard

Standardizer - Molecular Cosmetics for Chemoinformatics

Jun 14, 2007 - Poster
A chemical compound can appear in various forms and its graphical representation often depends on the taste of the chemist. These variants are usually represented with different graphs in…
lib

Maximum Common Substructure Based Hierarchical Clustering

Jun 5, 2008 - 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…
markushh

Representation, searching & enumeration of Markush structures - from molecules towards patents - 2009 update

Aug 31, 2009 - Poster
Cheminformatics systems usually focus primarily on handling specific molecules and reactions. However, Markush structures are also indispensable in various areas, like combinatorial libra…
reactor

How can generic reactions be specific? Virtual synthesis with “smart” reactions.

Apr 1, 2004 - Poster
High throughput screening initiated a new gold-rush in drug discovery. Although the reef of combinatorial chemistry has enriched the pharmaceutical industry with many new biologically act…
pka

A method for calculating the pKa values of small and large molecules

Jun 14, 2007 - Poster
A method was developed for predicting of the aqueous ionization constants (pK ) of organic molecules. The method is a based on empirically calculated physico-chemical parameters that are …
space

MarvinSpace: molecule visualisation application and toolkit

Mar 16, 2006 - Poster
An ever increasing number of molecular structure visualization tools are being developed by cheminformatics companies, academic research labs and recently by the open source community. Ma…
virtualscreen

Virtual screening using active set dependent optimization of dissimilarity metrics

Sep 11, 2003 - Poster
The efficiency of virtual screening in drug discovery greatly depends on three factors: (1) pharmacophore point perception (2) representation of molecular structures with a descriptor, (3…
markush

Representation, searching and enumeration of Markush structures - from molecules towards patents

Jun 5, 2008 - Poster
Cheminformatics systems usually focus primarily on handling specific molecules and reactions. However, Markush structures are also indispensable in various areas, like combinatorial libra…
jlust

Structure Based Clustering of NCI's Anti-HIV Library

Jul 5, 2001 - 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…
ct

Making real molecules in virtual space

Mar 15, 2005 - Poster
The computational description of chemical structures is a well established area. The field of synthetic chemistry, however, still does not have adequate software tools, since preparative …
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