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P071 - GCB 2005 - German Conference on Bioinformatics

https://dl.gi.de/handle/20.500.12116/24920
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Auflistung P071 - GCB 2005 - German Conference on Bioinformatics nach Erscheinungsdatum

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  • Konferenzbeitrag
  • Konferenzbeitrag
    Memory efficient folding algorithms for circular RNA secondary structures
    (German Conference on Bioinformatics 2005 (GCB 2005), 2005) Hofacker, Ivo L.; Stadler, Peter F.
    A small class of RNA molecules, in particular the tiny genomes of viroids, are circular. Yet most structure prediction algorithms handle only linear RNAs. The most straightforward approach is to compute circular structures from "internal" and "external" substructures separated by a base pair. This is incompatible, however, with the memory-saving approach of the Vienna RNA Package which builds a linear RNA structure from shorter (internal) structures only. Here we describe how circular secondary structures can be obtained without additional memory requirements as a kind of "post-processing" of the linear structures.
  • Konferenzbeitrag
    Invited talk: linkage disequilibrium sharing and tagSNP portability between populations
    (German Conference on Bioinformatics 2005 (GCB 2005), 2005) Jin, Li
  • Konferenzbeitrag
    Generation of 3D templates of active sites of proteins with rigid prosthetic groups
    (German Conference on Bioinformatics 2005 (GCB 2005), 2005) Nebel, Jean-Christophe
    With the increasing availability of protein structures, the generation of biologically meaningful 3D patterns from their simultaneous alignment is an exciting prospect: active sites could be better understood, protein functions and structures could be predicted more accurately. Although patterns can be generated at the fold and topological levels, no system produces high resolution 3D patterns including atom and cavity positions. Here, we present a new approach allowing the generation of 3D patterns from alignment of proteins with rigid prosthetic groups. Using 237 proteins representing these proteins, our method was validated by comparing 3D templates generated from homologues with structures of the proteins they model. Atom positions were predicted reliably: 93% of them had an accuracy below 1.00 Å. Similar results were obtained regarding chemical group and cavity positions. Finally, a 3D template was generated for the active site of human cytochrome P450 CYP17. Its analysis showed it is biologically meaningful: our method detected the main patterns and motifs of the P450 superfamily. The 3D template also suggested the locations of a cavity and of a hydrogen bond between CYP17 and its substrates. Comparisons with independently generated 3D models comforted these hypotheses.
  • Konferenzbeitrag
    Invited talk: chemistry meets biology: chemogenomics in drug discovery
    (German Conference on Bioinformatics 2005 (GCB 2005), 2005) Kubinyi, Hugo
  • Konferenzbeitrag
    Using residue propensities and tightness of fit to improve rigid-body protein-protein docking
    (German Conference on Bioinformatics 2005 (GCB 2005), 2005) Huang, Bingding; Schroeder, Michael
    Protein-protein interactions are fundamental as many proteins mediate their biological function through protein interactions. Over the past 20 years there have been many computational approaches to dock proteins. These approaches are mostly based on the shape complementarity of structures and the physio-chemical properties of the interfaces. However, these docking approaches are far from perfect and there still remains potential space to improve. We propose to use family-based residue interaction propensity as well as the tightness of fit between residues with high propensities as a scoring function to improve rigid body docking. This approach is evaluated on an established benchmark data set. Our scoring function improves the number of hits for enzyme-inhibitor complexes by a factor of 4-30 in comparison with shape complementarity alone and for antibodyantigen complexes by 4-11. The supplementary data are available at http://www.biotec.tu-dresden. de/\~bhuang/bdock.
  • Konferenzbeitrag
    Composite module analyst: A fitness-based tool for prediction of transcription regulation
    (German Conference on Bioinformatics 2005 (GCB 2005), 2005) Kel, Alexander; Konovalova, Tatiana; Waleev, Tagir; Cheremushkin, Evgeny; Kel-Margoulis, Olga; Wingender, Edgar
    Functionally related genes involved in the same molecular-genetic, biochemical, or physiological process are often regulated coordinately Such regulation is provided by precisely organized binding of a multiplicity of special proteins (transcription factors) to their target sites (cis-elements) in regulatory regions of genes. Cis-element combinations provide a structural basis for the generation of unique patterns of gene expression. Here we present a new approach for defining promoter models based on composition of transcription factor binding sites and their pairs. We utilize a multicomponent fitness function for selection of that promoter model fitting best to the observed gene expression profile. We demonstrate examples of successful application of the fitness function with the help of a genetic algorithm for the analysis of functionally related or co-expressed genes as well as testing on simulated data.
  • Konferenzbeitrag
    Invited talk: proteins of SARS coronavirus - experimental and theoretical studies
    (German Conference on Bioinformatics 2005 (GCB 2005), 2005) Hilgenfeld, Rolf
  • Konferenzbeitrag
    Inferring regulatory systems with noisy pathway information
    (German Conference on Bioinformatics 2005 (GCB 2005), 2005) Spieth, Christian; Streichert, Felix; Speern, Nora; Zell, Andreas
    With increasing number of pathways available in public databases, the process of inferring gene regulatory networks becomes more and more feasible. The major problem of most of these pathways is that they are very often faulty or describe only parts of a regulatory system due to limitations of the experimental techniques or due to a focus specifically only on a subnetwork of a larger process. To address this issue, we propose a new multi-objective evolutionary algorithm in this paper, which infers gene regulatory systems from experimental microarray data by incorporating known pathways from publicly available databases. These pathways are used as an initial template for creating suitable models of the regulatory network and are then refined by the algorithm. With this approach, we were able to infer regulatory systems with incorporation of pathway information that is incomplete or even faulty.
  • Konferenzbeitrag
    From greedy to branch & bound and back: assessing optimization strategies for incremental construction molecular docking tools
    (German Conference on Bioinformatics 2005 (GCB 2005), 2005) Griewel, Axel; Rarey, Matthias
    A branch & bound approach for the assembly-phase of the incremental construction algorithm of the software package FlexX is presented. For this a local bound for partial solutions has been implemented which estimates the best score achievable for the considered solutions. This estimation is based on scoring values which single components can achieve in certain regions of the active site as well as distance constraints deduced from the composition of the considered partial solution. Furthermore, a timeand space-bounded search strategy specific to the addressed problem has been developed. The implemented algorithm was tested on a dataset containing 169 complexes. In 116 of these cases the calculation was finished in a reasonably defined time frame while the calculation for the remaining complexes was not completed in this period of time. For all calculated complexes, the best solution shows a score better or equal to the solution of standard-FlexX. This, however, is not always associated with an improvement of the RMSD between the calculated placement of the ligand and the crystal structure. The presented algorithm is applicable for thorough virtual screening of small sets of ligands comprising up to nine rotatable, acyclic bonds. Furthermore, the method gives important insights to the k-greedy method and can be used for scientific assessment of new scoring functions within FlexX.