Journal Publications

N. Weskamp, D. Kuhn, E. Hüllermeier, G. Klebe.
Efficient similarity search in protein structure databases by k-clique hashing.
Bioinformatics 20(10), pages 1522-1526, 2004.

R. Balasubramaniyan, E. Hüllermeier, N. Weskamp, J. Kämper.
Clustering of Gene Expression Data Using a Local Shape-Based Similarity Measure.
Bioinformatics 21(7), pages 1069-1077, 2005.

D. Kuhn, N. Weskamp, S. Schmitt, E. Hüllermeier, G. Klebe.
From the Similarity Analysis of Protein Cavities to the Functional Classification of Protein Families Using Cavbase.
Journal of Molecular Biology, 359(4), pages 1023-1044, 2006.

N. Weskamp, E. Hüllermeier, D. Kuhn, G. Klebe.
Multiple Graph Alignment for the Structural Analysis of Protein Active Sites.
ACM/IEEE Transactions on Computational Biology and Bioinformatics, 4(2), pages 310-320, 2007.

P. Block, N. Weskamp, A. Wolf, G. Klebe.
Strategies to Search and Design Stabilizers of Protein-Protein Interactions: a Feasibility Study.
Proteins: Structure, Function, and Bioinformatics, 68 (1), pages 170-186, 2007.

D. Kuhn, N. Weskamp, E. Hüllermeier, G. Klebe.
Functional Classification of Protein Kinase Binding Sites using Cavbase.
ChemMedChem, 2 (10), pages 432 - 1447, 2007.

M. Wawer, L. Peltason, N. Weskamp, A. Teckentrup, J. Bajorath.
Structure-Activity Relationship Anatomy by Network-like Similarity Graphs and Local Structure-Activity Relationship Indices.
Journal of Medicinal Chemistry, 51 (19), pages 6075-84, 2008.

N. Weskamp, E. Hüllermeier, G. Klebe.
Merging Chemical and Biological Space: Structural Mapping of Enzyme Binding Pocket Space.
Proteins: Structure, Function and Bioinformatics, 76 (2), pages 317-330, 2009.

L. Peltason, N. Weskamp, A. Teckentrup, J. Bajorath.
Exploration of Structure.Activity Relationship Determinants in Analogue Series.
Journal of Medicinal Chemistry, 52 (10), pages 3212-3224, 2009.

A. Wassermann, P. Haebel, N. Weskamp, J. Bajorath.
SAR matrices: automated extraction of information-rich SAR tables from large compound data sets.
Journal of Chemical Information and Modeling, 52 (7), pages 1769-1776, 2012.

J. Fuchs, B. Wellenzohn, N. Weskamp, K. Liedl.
Matched Peptides: Tuning Matched Molecular Pair Analysis for Biopharmaceutical Applications.
Journal of Chemical Information and Modeling, 55 (11), pages 2315-2323, 2015.

N. Weskamp.
Guided Iterative Substructure Search (GI-SSS) - A New Trick for an Old Dog.
Molecular Informatics, 35 (6-7), pages 286-292, 2016.

Book Chapters

B. Beck, M. Bieler, P. Haebel, A. Teckentrup, A. Weber, N. Weskamp.
Applications of Cheminformatics in Pharmaceutical Research: Experiences at Boehringer Ingelheim in Germany.
in: J. Bajorath (Ed.), Chemoinformatics in Drug Discovery, Wiley, 2014.

Invited Talks

N. Weskamp.
Cavbase: A tool for large-scale analysis of protein binding pockets and their occupants.
International Workshop: New Approaches in Drug Design & Discovery, Rauischholzhausen, Germany, March 21-24, 2005.

N. Weskamp.
Cavbase: A tool for large-scale analysis of protein binding pockets and their occupants.
BioSys workshop on Chemogenomics in Drug Development, Lyngby, Denmark, November 11, 2005.

N. Weskamp.
Structure-based Mapping of Protein Binding Pocket Space.
MODREF 2006, Barcelona, Spain, July 3-5, 2006.

N. Weskamp.
KNIME as a platform for distributed molecular property predictions.
4th KNIME User Group Meeting, Zurich, Switzerland, March 2-4, 2011.

N. Weskamp.
Workflow Mining: Identification of frequent patterns in a large collection of KNIME workflows.
5th KNIME User Group Meeting, Zurich, Switzerland, February 1-3, 2012.

N. Weskamp.
Leveraging a company's knowledge base to stimulate drug discovery innovation.
Life Science R&D Big Data Leaders Forum, Berlin, Germany, December 11-12, 2014.

N. Weskamp.
KNIME for the Masses: Flexible and Scalable Deployment of KNIME-Workflows.
8th KNIME User Group Meeting, Berlin, Germany, February 25-27, 2015.

Reviewed Publications in Conference Proceedings

J. Berthold, U. Klusik, R. Loogen, S. Priebe, N. Weskamp.
High-level Process Control in Eden.
In H. Kosch et al. (Hrsg.): Euro-Par 2003. Parallel Processing: 9th International Euro-Par Conference, Klagenfurt, Austria, August 26-29, 2003. Proceedings, pages 732-741.
LNCS 2790, © 2003 Springer.

N. Weskamp, D. Kuhn, E. Hüllermeier, G. Klebe.
Efficient Similarity Search in Protein Structure Databases: Improving Clique-Detection through Clique Hashing.
In H.-W. Mewes et al. (eds.): GCB 03. German Conference on Bioinformatics 2003, Proceedings - Volume I, pages 179-184.
belleville Verlag, München, ISBN: 3-936-298-80-7.

N. Weskamp, E. Hüllermeier, D. Kuhn, G. Klebe.
Graph Alignments: A New Concept to Detect Conserved Regions in Protein Active Sites.
In R. Giegerich, J. Stoye (eds.), Proceedings German Conference on Bioinformatics 2004, pages 131-140.
GI-Lecture Notes in Informatics, Bonn, ISBN: 3-88579-382-2.

Presentations at Informal Workshops

J. Berthold, R. Loogen, S. Priebe, N. Weskamp.
Porting the Eden System to GHC 5.00.
In T. Arts and R. Peña: Proceedings of IFL 2002.
TR 127-02, Universidad Complutense de Madrid.

Technical Reports

N. Weskamp, Eyke Hüllermeier, Daniel Kuhn, Gerhard Klebe.
Graph Alignment: Robust Data Mining on Structured Objects.
Technical Report No. 41, Department of Mathematics and Computer Science, Philipps-University Marburg.

E. Hüllermeier, N. Weskamp, D. Kuhn, G. Klebe.
Wissensentdeckung in strukturbasierten Daten: Graph Alignment zur Analyse von Proteinstrukturen.
Manuscript in preparation.

Theses

N. Weskamp.
Effiziente Algorithmen und Datenstrukturen zur Ähnlichkeitssuche in Proteinstrukturdatenbanken.
Masters Thesis, Department of Mathematics and Computer Science, Philipps-University Marburg

N. Weskamp.
Efficient Algorithms for Robust Pattern Mining on Structured Objects with Applications to Structure-Based Drug Design.
PhD Thesis, Department of Mathematics and Computer Science, Philipps-University Marburg