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Software using JOELib/JOELib2

Here is a list of software using the JOELib library. We would be proud to add you to this list, if you will send us an E-Mail.

Name Description
Cheminformatics  
JCompChem Internal developments of efficient algorithms and descriptors:
  • model building (regression and classification) and clustering algorithms in combination with efficient feature selection algorithms
  • maximum common substructure (MCS) search (see also page of Jörg Wegner)
  • kernel based molecule similarity (see also page of Holger Fröhlich)
  • multi-objective combinatorial library design (see also page of Felix Streichert)
ChemMine ChemMine is a compound mining database that facilitates drug and agrochemical discovery and chemical genomics screens.
LAZAR - Predictive Toxicology lazar (Lazy Structure-Activity Relationships) is a tool for the prediction of toxic activities of chemical structures.
QSAR Quantitative Structure Activity Relationship (QSAR) project
Compumine Machine learning rule discovery system for ADMET prediction, which can work with any kind of descriptors. JOELib is here used for demo purpose.
COFEA High speed searching methods using the Compressed Feature Matrix
Chemical Development Kit (CDK) Java interface to the CDK without descriptor values and chirality informations.
Bioinformatics  
Biocatalysis/Biodegradation Microbial biocatalytic reactions and biodegradation pathways primarily for xenobiotic, chemical compounds. They are using JOELib for their pathway prediction engine using transformation rules.

JOELib/JOELib2: Presentations and Publications using it

Assignment Kernels For Chemical Compounds
H. Fröhlich, J. K. Wegner, A. Zell
International Joint Conference on Neural Networks (IJCNN), in Montréal, Québec, Canada, July 31-August 4, 2005.
Full scientific program
 
Comparing Vector Versus Structural Coding for Predicting ADMETox Data Sets
J. K. Wegner, H. Fröhlich, A. Zell
The 7th International Conference on Chemical Structures, in Noordwijkerhout, The Netherlands, CA, June 5–9, 2005. Session: Structure-Activity and Structure-Property Prediction (Chair: Markus Wagener). Organisations: CINF, CSA Trust, CSJ, GDCh, KNCV, RSC, and SCS
Full scientific program
 
Relevance of feature selection for clustering
J. K. Wegner, H. Fröhlich, F. Sieker, A. Zell
International Workshop New Approaches in Drug Design & Discovery, Marburg, Germany, March 21-24, 2005.
Poster
 
Difference in vector-based and graph-based coding for ADME prediction.
J. K. Wegner, A. Zell
The 229th ACS National Meeting, in San Diego, CA, March 13-17, 2005. Session: ADME/tox Informatics (Chair: O. F. Güner). Organisation: American Chemical Society (ACS)-Division of Computers in Chemistry
Abstract, Session program,Full scientific program

Relevance of feature selection for clustering molecules.
J. K. Wegner, F. Sieker, A. Zell
The 229th ACS National Meeting, in San Diego, CA, March 13-17, 2005. Session: Applications of Information Theory in Chemistry (Chair: V. Shanmugasundaram and G. M Maggiora). Organisation: American Chemical Society (ACS)-Division of Computers in Chemistry
Abstract, Session program, Full scientific program

JOELib - An open source chemoinformatics library for data mining and graph mining on molecular structures.
J. K. Wegner
invited presentation at eCheminfo 2004, 8-19 November, Applications of Cheminformatics and Modelling to Drug Discovery. Session: Open Source (Chair: G. Morris). Organisation: Douglas Connect
Abstract, Full scientific program (HTML, PDF)

Data Mining and Generalisation Ability on Molecular Structures.
J. K. Wegner, H. Mielenz
CIC Workshop 2004 - Neue Entwicklungen in der Chemoinformatik, 14.-16. November, Germany . Session: Pharmazeutische Chemoinformatik (Chair: G. Schneider). Organisation: Gesellschaft Deutscher Chemiker (GDCh)
Full scientific program (HTML, PDF)

Data preparation and feature selection for chemical data sets - Building ’general’ models.
J. K. Wegner
invited presentation at Analytica Conference 2004, 11.-13. May, Munich, Germany. Session: Molecular Informatics for a Deeper Insight (Chair: C. Steinbeck). Organisation:
Abstract, Full scientific program
Towards Optimal Descriptor Subset Selection with Support Vector Machines in Classification and Regression
H. Fröhlich, J. K. Wegner, A. Zell
QSAR Comb. Sci., 2004, 23, 311-318.
DOI: 10.1002/qsar.200410011
Feature selection for Descriptor based Classification Models. 1. Theory and GA-SEC Algorithm
J. K. Wegner, H. Fröhlich, A. Zell
Journal of Chemical Information and Computer Science (JCICS), 2004, 44, 921-930.
Abstract, DOI: 10.1021/ci0342324
Feature selection for Descriptor based Classification Models. 2. Human Intestinal Absorption (HIA)
J. K. Wegner, H. Fröhlich, A. Zell
Journal of Chemical Information and Computer Science (JCICS), 2004, 44, 931-939.
Abstract, DOI: 10.1021/ci034233w
Prediction of Aqueous Solubility and Partition Coefficient Optimized by a Genetic Algorithm Based Descriptor Selection Method
J. K. Wegner, A. Zell
Journal of Chemical Information and Computer Science (JCICS), 2003, 43(3), 1077-1084.
Abstract, DOI: 10.1021/ci034006u
The Compressed Feature Matrix - A fast method for feature based substructure search
S.F.Badreddin Abolmaali, Jörg K. Wegner, Andreas Zell
Journal of Molecular Modeling, 2003, 9, 235-241.
Abstract, DOI: 10.1007/s00894-003-0126-0
The Chemistry Development Kit (CDK): An Open-Source Java Library for Chemo- and Bioinformatics
C. Steinbeck, Y. Han, S. Kuhn, O. Horlacher, E. Luttmann, E. Willighagen
Journal of Chemical Information and Computer Science (JCICS), 2003, 43(3), 1077-1084.
Abstract, DOI: 10.1021/ci025584y
The University of Minnesota Biocatalysis/Biodegradation Database: Post-Genomic Datamining
L.B.M. Ellis, B.K. Hou, W. Kang, L.P. Wackett
Nucleic Acids Research, 2003, 31, 262-265.
Abstract
The Compressed Feature Matrix - A novel descriptor for adaptive similarity search
S.F.Badreddin Abolmaali, Claude Ostermann, Andreas Zell
Journal of Molecular Modeling, 2003, 9, 66-75.
Abstract, DOI: 10.1007/s00894-002-0110-0
Building QSAR models using shannon entropy and a genetic algorithm
Jörg K. Wegner, Andreas Zell
17. Molecular-Modelling Workshop, Erlangen, Germany, May 27-28, 2003.
Poster

JOELib-Eine plattformunabhängige computational chemistry-Bibliothek in Java
Jörg K. Wegner, Andreas Zell
16. Molecular-Modelling Workshop, Erlangen, Germany, May 07-08, 2002.
Poster
A New Method to Estimate Ligand-Receptor Energetics
J. R. Bock and D. A. Gough
Molecular & Cellular Proteomics, 2002, 1, 904-910.
Abstract, DOI: 10.1074/mcp.M200054-MCP200

3DPOPS: From carbohydrate sequence to 3D structure
R. Nordström
Dissertation, Department of Computer Science, University of Skövde, Sweden, 2002.
Online version.

Publications caused by teaching cheminformatics :-)

Lead discovery and lead optimization (drug design) algorithms, Various brilliant authors, Leadership J. K. Wegner

 


Last changes: 08.12.2010, 17:03 CET (UTC/GMT +1 hour) wegner.
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