Escherichia coli (E. coli) bacteria can damage DNA of the gut lining cells and may encourage the development of colon cancer according to recent reports. Genetic switches are specific sequence motifs and many of them are drug targets. It is interesting to know motifs and their location in sequences. At the present study, Gibbs sampler algorithm was used in order to predict and find functional m...

Membrane proteins are important for many processes in the cell and used as main drug targets. The increasing number of high-resolution structures available makes for the first time a characterization of local structural and functional motifs in alpha-helical transmembrane proteins possible. MeMotif (http://projects.biotec.tu-dresden.de/memotif) is a database and wiki which collects more than 20...

Topological network motifs represent functional relationships within and between regulatory and protein-protein interaction networks. Enriched motifs often aggregate into self-contained units forming functional modules. Theoretical models for network evolution by duplication-divergence mechanisms and for network topology by hierarchical scale-free networks have suggested a one-to-one relation b...

The paper presents a method for discovery of speciÞc types of rules related to detection and extraction of explicit potentially biologically active DNA motifs from nucleotide databases. The characteristic of these rules is that they represent a relation of the strengths of signals of two motifs and their mutual distance. The rule extraction is based on a genetic algorithm. The method is applied...

The Msn2 and Msn4 transcription factors play crucial roles in the yeast general stress response. Previous studies identified several large functional domains of Msn2, mainly through crude truncations. Here, using bioinformatics and experimental approaches to examine Msn2 structure-function relationships, we have identified new functional motifs in the Msn2 transcriptional-activating domain (TAD...

Structural genomics initiatives are beginning to rapidly generate vast numbers of protein structures. For many of the structures, functions are not yet determined and high-throughput methods for determining function are necessary. Although there has been extensive work in function prediction at the sequence level, predicting function at the structure level may provide better sensitivity and pre...

Prediction of functional peptide motifs from sequences is an important problem in bioinformatics. Experimental discovery of functional sequences is laborious. Searches for specific motifs within the increasing number of proteins available in public databases often involve extensive computer calculations. Short peptide motifs are especially hard to identify via currently available methods. Prese...

cluster dileucine motif to the VHS domain in an extended New structures of LD motifs bound to the focal adheconformation, highlighting the structural diversity of sion targeting domain show that the motifs are recogAspand Leu-containing signaling motifs. nized as amphipathic helices. The structures highAs with most other pairings between domains and light the structural and functional diversity...