Small molecule similarity modeling and clustering for Richter Richter Gedeon Ltd. 2004-2006.
Molecules are easy to be represented by labeled graphs. Unfortunately, this representation is not very suitable for computing similarity between molecules.
Therefore, fingerprint models are applied to solve this problem much more efficiently.
Metabolic networks are under continuous evolution. Most organism have a common set of reactions as a part of their metabolic networks that relate to essential processes but a large proportion of the reactions present in different organisms are specific to the needs of individual organisms or tissues. The regions of metabolic networks corresponding to these non-essential reactions are under continuous evolution.
Reticular Alignment is our new method for for multiple sequence alignment. Unlike previous corner-cutting methods, our approach does not define a compact part of the dynamic programming table. Instead, it defines a set of optimal and suboptimal alignments at each step during the progressive alignment. The set of alignments are represented with a network to store them and use them during the progressive alignment in an efficient way.
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