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.
J. Jimenez-Luna, M. Skalic, N. Weskamp, G. Schneider.
Coloring Molecules with Explainable Artificial Intelligence for Preclinical Relevance Assessment.
Journal of Chemical Information and Modeling, 61 (3), pages 1083-1094, 2021.
J. Jimenez-Luna, F. Grisoni N. Weskamp, G. Schneider.
Artificial intelligence in drug discovery: recent advances and future perspectives.
Expert Opinion on Drug Discovery, 16 (9), pages 949-959, 2021.
J. Jimenez-Luna, M. Skalic, N. Weskamp.
Benchmarking molecular feature attribution methods with activity cliffs.
Journal of Chemical Information and Modeling, accepted, 2022.
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