Publications

Full Papers

ChEMBLSpace - a graphical explorer of the chemogenomic space covered by the ChEMBL database
Nikolas Fechner, George Papadatos, David Evans, John Richard Morphy, Suzanne Clare Brewerton, David Thorner, and Michael Bodkin
Bioinformatics, 2012,29 (4), 523-524 Abstract DOI: 10.1093/bioinformatics/bts711
Large-scale learning of structure-activity relationships using a linear support vector machine and problem-specific metrics
Georg Hinselmann, Lars Rosenbaum, Andreas Jahn, Nikolas Fechner, Claude Ostermann, and Andreas Zell
Journal of Chemical Information and Modeling, 2011, 52, 203-213 Abstract DOI: 10.1021/ci100073w
jCompoundmapper: An open source java library and command-line tool for chemical fingerprints.
Georg Hinselmann, Lars Rosenbaum, Andreas Jahn, Nikolas Fechner, and Andreas Zell
Journal of Cheminformatics, 2011, 3(3) Abstract, PDF, DOI: 10.1186/1758-2946-3-3
Boltzmann-enhanced flexible atom-pair kernel with dynamic dimension reduction
Andreas Jahn, Georg Hinselmann, Lars Rosenbaum, Nikolas Fechner, and Andreas Zell
Molecular Informatics, 2011, accepted
Approximation of graph kernel similarities for chemical graphs by kernel principal component analysis
Georg Hinselmann, Andreas Jahn, Nikolas Fechner, Lars Rosenbaum, and Andreas Zell
in Lecture Notes in Computer Science (EvoBIO 2011) , Springer-Verlag Berlin Heidelberg, 2011, 6623, pp. 123-134
A Free-Wilson-like approach to analyze QSAR models based on graph decomposition kernels
Nikolas Fechner, Georg Hinselmann, Andreas Jahn, Lars Rosenbaum, and Andreas Zell
Molecular Informatics, 2010, 29, 491-497 Abstract DOI: 10.1002/minf.201000053
Estimation of the applicability domain of kernel-based machine learning models for virtual screening
Nikolas Fechner, Andreas Jahn, Georg Hinselmann and Andreas Zell
Journal of Cheminformatics, 2010, 2:2 Abstract, PDF, DOI: 10.1186/1758-2946-2-2
Probabilistic Modeling of Conformational Space for 3D Machine Learning Approaches
Andreas Jahn, Georg Hinselmann, Nikolas Fechner, Carsten Henneges, and Andreas Zell
Molecular Informatics, 2010, 29(5),441-455
Graph Kernels for Chemical Compounds Using Topological and Three-Dimensional Local Atom Pair Environments
Georg Hinselmann, Nikolas Fechner, Andreas Jahn and Andreas Zell
Elsevier Neurocomputing, 2010, in press
Optimal assignment methods for ligand-based virtual screening
Andreas Jahn, Georg Hinselmann, Nikolas Fechner and Andreas Zell
Journal of Cheminformatics, 2009, 1:14 Abstract, PDF, DOI: 10.1186/1758-2946-1-14
Atomic local neighborhood flexibility incorporation into a structured similarity measure for QSAR
Nikolas Fechner, Andreas Jahn, Georg Hinselmann and Andreas Zell
in Journal of Chemical Information and Modeling, 2009, 49 (3), pp 549-560 DOI: 10.1021/ci800329r
Chronic Rat Toxicity Prediction of Chemical Compounds using Kernel Machines
Georg Hinselmann, Andreas Jahn, Nikolas Fechner and Andreas Zell
in Lecture Notes in Computer Science (EvoBIO 2009) , Springer-Verlag Berlin Heidelberg, 2009, 5483, pp. 25-36
DOI: 10.1007/978-3-642-01184-9_3
Comparison of Different Approaches to Vibration-based Terrain Classification
Christian Weiss, Nikolas Fechner, Matthias Stark and Andreas Zell
in Proceedings of the 3rd European Conference on Mobile Robots (ECMR 2007), Freiburg, Germany, September 19-21, 2007, pp. 7-12

Book Chapters

Molecular Descriptors
Nikolas Fechner, Georg Hinselmann, and Jörg K. Wegner
Handbook of Chemoinformatics Algorithms
Chapman & Hall/CRC Mathematical & Computational Biology, to appear 2010

Abstracts

Assessing the selectivity of serine proteases inhibitors using structural similarity
Nikolas Fechner, Andreas Jahn, Georg Hinselmann and Andreas Zell
in Chemistry Central Journal, 2009, 3(Suppl 1), P10. Abstract, DOI: 10.1186/1752-153X-3-S1-P10
An extension of the pharmacophore kernel using radial atomtype fingerprints
Georg Hinselmann, Matthias Eckert, Thomas Holder, Andreas Jahn, Nikolas Fechner and Andreas Zell
in Chemistry Central Journal, 2009, 3(Suppl 1), P11. Abstract, DOI: 10.1186/1752-153X-3-S1-P11
Two-step hierarchical assignments on molecular graphs
Andreas Jahn, Nikolas Fechner, Georg Hinselmann and Andreas Zell
in Chemistry Central Journal, 2009, 3(Suppl 1), P13. Abstract, DOI: 10.1186/1752-153X-3-S1-P13
Estimating the applicability domain of kernel based QSPR models using classical descriptor vectors
Nikolas Fechner, Georg Hinselmann, Christina Schmiedl and Andreas Zell
in Chemistry Central Journal, 2008, 2(Suppl 1), P2. Abstract, DOI: 10.1186/1752-153X-2-S1-P2
Beyond descriptor vectors: QSAR modelling using structural similarity
Andreas Zell, Georg Hinselmann, Nikolas Fechner and Andreas Jahn
in Chemistry Central Journal, 2008, 2(Suppl 1), S3. Abstract, DOI: 10.1186/1752-153X-2-S1-S3

Presentations

Incorporating Molecular Flexibility into three-dimensional Structural Kernels
A. Jahn, N. Fechner, G. Hinselmann and Andreas Zell
4. German Conference on Cheminformatics, 9-11. November 2008, Goslar
Altered Ligands for Heterodimers of Toll-Like Receptors 1 and 2
K.-H. Wiesmüller, S. Voss, G. Hinselmann, N. Fechner, R. Spohn and Andreas Zell
12th Japanese-German Symposium on Peptide Science, Akabori, Japan.
Beyond Descriptor Vectors: QSAR Modelling with structural similarity measures
G. Hinselmann, N. Fechner, A. Jahn and A. Zell
3. German Conference on Cheminformatics, 11-13. November 2007, Goslar

Poster

Kernel-based Estimation of the Applicability Domain of QSAR models
N. Fechner, G. Hinselmann, A. Jahn, A. Zell
presented on the German Conference on Chemoinformatics 2009
Assessing the Selectivity of Serine Proteases Inhibitors using Structural Similarity
N. Fechner, A. Jahn, G. Hinselmann, A. Zell
presented on the German Conference on Chemoinformatics 2008
Two-Step Hierarchical Assignments on Molecular Graphs
A. Jahn, N. Fechner, G. Hinselmann, A. Zell
presented on the German Conference on Chemoinformatics 2008
Extending Pharmacophore Kernels with Radial Fingerprint Environments
G. Hinselmann, M. Eckert, T. Holder, A. Jahn, N. Fechner, A. Zell
presented on the German Conference on Chemoinformatics 2008
Altered Ligands for Heterodimers of Toll-Like Receptors 1 and 2
S. Voss, D. Bächle, R. Spohn, G. Hinselmann, N. Fechner, A. Zell, A.J. Ulmer and K.-H. Wiesmüller, 
presented at the  IEIIS 2008, Edingburgh, Scottland
Estimating the Applicability Domain of Kernel based QSPR Models using Classical Descriptor Vectors
N. Fechner, G. Hinselmann, C. Schmiedl, A. Zell
presented on the German Conference on Chemoinformatics 2007
Structural Similarity Measures with Kernel Properties for Ligand based Virtual Screening
N. Fechner, G. Hinselmann, A. Zell
presented on the NAD Workshop 2007 at Rauischholzhausen
Implicitly Defined Substructure Fingerprints for Support Vector Machines
N. Fechner, G. Hinselmann, A. Zell
presented on the German Conference on Chemoinformatics 2006
In Silico Lead-Structure Proposal with Filters using Support Vector Machines and Implicit Defined Substructure Fingerprints
N. Fechner, G. Hinselmann, A. Zell
presented on the German Conference on Bioinformatics 2006

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