Algorithmic Cheminformatics

My main research area is Algorithmic Cheminformatics, see http://cheminf.imada.sdu.dk/mod/index.html for more details. See http://cheminf.imada.sdu.dk/mod/playground.html for an online version of our cheminformatics software MØD, which heavily relies on the double pushout approach for graph rewriting.

Double Pushout Approach

Selected References

A Generic Framework for Engineering Graph Canonization Algorithms Jakob L. Andersen, Daniel Merkle, 2018 Proceedings of the Twentieth Workshop on Algorithm Engineering and Experiments (ALENEX), 2018 [ DOI |TR ]

Finding the K best synthesis plans Rolf Fagerberg, Christoph Flamm, Rojin Kianian, Daniel Merkle and Peter F. Stadler, J Cheminform (2018) 10:19, [ DOI |PDF ]

Rule Composition in Graph Transformation Models of Chemical Reactions Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler, MATCH, Communications in Mathematical and in Computer Chemistry, 80(3), 661-704, 2018 [HTTP]

Chemical Transformation Motifs — Modelling Pathways as Integer Hyperflows Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2017 [ DOI | TR ]

An Intermediate Level of Abstraction for Computational Systems Chemistry Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler, Philosophical Transactions of the Royal Society of London A: Mathematical, Physical and Engineering Sciences, 375(2109), 2017 [ DOI | TR ]