http://dl.gi.de/handle/20.500.12116/22357 2026-07-23T16:01:35Z http://dl.gi.de/handle/20.500.12116/22377 Understanding of SMFS barriers by means of energy profiles Dressel, Frank; Marsico, Annalisa; Tuukkanen, Anne; Schroeder, Michael; Labudde, Dirk Falter, Claudia; Schliep, Alexander; Selbig, Joachim; Vingron, Martin; Walther, Dirk In the last years, Single Molecule Force Spectroscopy was more and more used to gain insight into the fundamental principles behind protein structure and stability. Nevertheless, the interpretation of the experimental findings is not so easy and additional computational approaches are needed to interpret them. Here, we proposed an approach based on interaction patterns between amino acids to explain the emergence of SMFS unfolding barriers in the experiment. With our approach, we can predict around 64% of the experimentally detectable barriers. 2007-01-01T00:00:00Z http://dl.gi.de/handle/20.500.12116/22376 Protein structure comparison based on fold evolution Kurbatova, Natalja; Mančinska, Laura; Vīksna, Juris Falter, Claudia; Schliep, Alexander; Selbig, Joachim; Vingron, Martin; Walther, Dirk The paper presents a protein structure comparison algorithm that is capable to identify specific fold mutations between two proteins. The search for such mutations is based on structure evolution models suggesting that, similarly as sequences, protein folds (at least partially) evolve by a stepwise process, where each step comprises comparatively simple changes affecting few secondary structure elements. The particular fold mutations considered in this study are based on the work by Grishin [Gr01]. The algorithm uses structure representation by 3D graphs and is a modification of a method used in SSM structure alignment tool [KH04a]. Experiments demonstrate that our method is able automatically identify 85% of examples of fold mutations given by Grishin. Also a number of tests involving all-against-all comparisons of CATH struc- tural domains have been performed in order to measure comparative frequencies of different types of fold mutations and some statistical estimations have been obtained. 2007-01-01T00:00:00Z http://dl.gi.de/handle/20.500.12116/22375 Tanimoto’s Best Barbecue: Discovering Regulatory Modules using Tanimoto Scores Menzel, Peter; Stadler, Peter F.; Mosig, Axel Falter, Claudia; Schliep, Alexander; Selbig, Joachim; Vingron, Martin; Walther, Dirk We present a combinatorial method for discovering cis-regulatory modules in promoter sequences. Our approach combines “sliding window” approaches with a scoring function based on the so-called Tanimoto score. This allows to identify sets of binding sites that tend to occur preferentially in the vicinity of each other in a given set of promoter sequences belonging to co-expressed or orthologous genes. We bench- mark our method on a data set derived from muscle-specific genes, demonstrating that our approach is capable of identifying modules that were identified as functional in previous studies. 2007-01-01T00:00:00Z http://dl.gi.de/handle/20.500.12116/22373 Identifying microRNAs and their targets Rajewsky, Nikolaus Falter, Claudia; Schliep, Alexander; Selbig, Joachim; Vingron, Martin; Walther, Dirk I will summarize what can be learned from predicting and analyzing microRNA targets. As an example, I will discuss the function of miR-150 in the immune system. Finally, I will present a new algorithm for the identification of microRNAs from deep sequencing data. 2007-01-01T00:00:00Z