Author: Ferenc Csizmadia

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…

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
urea

JChem AnalogMaker: A software for generating targeted novel synthetically feasible lead molecules

Apr 1, 2004 - Poster
JChem AnalogMaker is a program for de novo design and lead optimization. It uses an evolutionary search algorithm to optimize fragment-built molecules against a user customizable goal fun…
dissociation

Prediction of dissociation constant using microconstants

Apr 1, 2004 - Poster
A new method for predicting the aqueous ionization constants (pKa) of organic molecules has been developed in 2004. The method is based mainly on empirically calculated partial charges. H…
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…
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…
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…
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…
mspace

Web-enabled visualization of chemical structures

Aug 11, 2005 - Poster
An ever increasing number of molecular structure visualizaton tools are being developed by cheminformatics companies, academic research labs and recently by the open source community. Man…
oracle

JChem Cartridge: Cheminformatics Platform for Oracle

Jun 14, 2007 - 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…
noordwijkerhout

Handling of homology variation in structure representation, patent Markush search, enumeration and visualization

Jun 7, 2011 - Poster
Scientific poster on the International Conference on Chemical Structures in Noordwijkerhout: Cheminformatics systems usually focus on handling specific molecules and reactions. However, g…
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 …
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…
prediction

Prediction of distribution coefficient using microconstants

Apr 1, 2004 - Poster
A new method has been developed for predicting the octanolwater distribution coefficient of organic molecules. The prediction of log based on empirically calculated micro ionization const…
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…

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…
phwindow

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

Mar 29, 2007 - Poster
A method was developed for predicting of the aqueous ionization constants (pKa) of organic molecules. The method is a based on empirically calculated physico-chemical parameters that are …
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…
oszlop

Virtual Screening Using Fingerprints Part II. Enhanced Search by Optimized Dissimilarity Metrics

Aug 15, 2003 - Poster
A large compound database is explored for structures that bare a similarity to a few given query structures, where the molecular similarity refers to the match of chemical, pharmacologica…
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