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
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…
chemicalterms

Chemical Terms - Functions for Cheminformatics

Jun 5, 2008 - Poster
Pharmaceutical research is not just about molecules, it is about realizable molecules having certain properties. The available set of computable properties is growing, each function usual…
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…
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 …
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…
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 …
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…

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…
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…
screen3d

Flexible alignment in 3D & applications presented at ACS Fall meeting, Boston, 2010

Sep 10, 2010 - Presentation
Fully flexible 3D alignment method without the need for sampling the conformational space is presented. This approach offers advantages over methods that rely on multiple conformations. (…
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…
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…
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…
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 …
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…
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