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Improving profile-profile alignments via log average scoring 1

1st International Workshop on algorithms in Bioinformatics, WABI 2001

作者： Von Öhsen, Niklas Zimmer, Ralf SCAI-Institute for Algorithms and Scientific Computing GMD-German National Research Center for Information Technology Schloss Birlinghoven Sankt Augustin53754 Germany

ISBN: (数字)9783540446965

ISBN: (纸本)3540425160

Alignments of frequency profiles against frequency profiles have a wide scope of applications in currently used bioinformatic analysis tools ranging from multiple alignment methods based on the progressive alignment approach to detecting of structural similarities based on remote sequence homology. We present the new log average scoring approach to calculating the score to be used with alignment algorithms like dynamic programming and show that it significantly outperforms the commonly used average scoring and dot product approach on a fold recognition benchmark. The score is also applicable to the problem of aligning two multiple alignments since every multiple alignment induces a frequency profile. © Springer-Verlag Berlin Heidelberg 2001.

关键词： Dynamic programming

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Derivation of a scoring function for crystal structure prediction

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Acta Crystallographica Section A: Foundations of Crystallography 2001年第4期57卷 442-450页

作者： Apostolakis, Joannis Hofmann, Detlef Walter Maria Lengauer, Thomas Institute for Algorithms and Scientific Computing German National Research Center for Information Technology (GMD-SCAI) Birlinghoven 53754 Sankt Augustin Germany Department of Computer Science University of Bonn 53117 Bonn Römerstrasse 164 Germany

The ever increasing number of experimentally resolved crystal structures supports the possibility of fully empirical crystal structure prediction for small organic molecules. Empirical methods promise to be significantly more efficient than methods that attempt to solve the same problem from first principles. However, the transformation from data to empirical knowledge and further to functional algorithms is not trivial and the usefulness of the result depends strongly on the quantity and the quality of the data. In this work, a simple scoring function is parameterized to discriminate between the correct structure and a set of decoys for a large number of different molecular systems. The method is fully automatic and has the advantage that the complete scoring function is parametrized at once, leading to a self-consistent set of parameters. The obtained scoring function is tested on an independent set of crystal structures taken from the P1 and P1̄ space groups. With the trained scoring function and FlexCryst, a program for small-molecule crystal structure prediction, it is shown that approximately 73% of the 239 tested molecules in space group P1 are predicted correctly. For the more complex space group P1̄, the success rate is 26%. Comparison with force-field potentials indicates the physical content of the obtained scoring function, a result of direct importance for protein threading where such database-based potentials are being applied. © 2001 International Union of Crystallography.

关键词： scoring function crystal structure prediction functional algorithms.

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High-level data mapping for clusters of SMPs

High-level data mapping for clusters of SMPs

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International Symposium on Parallel and Distributed Processing (IPDPS)

作者： S. Benkner T. Brandes Institute for Software Science University of Technology Vienna Austria GMD-German National Research Center for Information Technology SCAI-Institute for Algorithms and Scientific Computing Saint Petersburg Russia

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Centralization: A new method for the normalization of gene expression data

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Bioinformatics 2001年第SUPPL_1期17卷 S323-S331页

作者： Zien, Alexander Aigner, Thomas Zimmer, Ralf Lengauer, Thomas SCAI - Institute for Algorithms and Scientific Computing GMD - German National Research Center for Information Technology Schloss Birlinghoven Sankt Augustin 53754 Germany Department of Pathology University of Erlangen-Nürnberg Erlangen 91054 Krankenhausstr. 8-10 Germany

Microarrays measure values that are approximately proportional to the numbers of copies of different mRNA molecules in samples. Due to technical difficulties, the constant of proportionality between the measured intensities and the numbers of mRNA copies per cell is unknown and may vary for different arrays. Usually, the data are normalized (i.e., array-wise multiplied by appropriate factors) in order to compensate for this effect and to enable informative comparisons between different experiments. Centralization is a new two-step method for the computation of such normalization factors that is both biologically better motivated and more robust than standard approaches. First, for each pair of arrays the quotient of the constants of proportionality is estimated. Second, from the resulting matrix of pairwise quotients an optimally consistent scaling of the samples is computed. © Oxford University Press 2001.

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A simple iterative approach to parameter optimization 00

A simple iterative approach to parameter optimization

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Proceedings of the fourth annual international conference on Computational molecular biology

作者： Alexander Zein Ralf Zimmer Thomas Lengauer GMD - German National Research Center for Information Technology Institute for Algorithms and Scientific Computing (SCAI) Schloβ Birlinghoven D-53754 Sankt Augustin Germany

ISBN: (纸本)9781581131864

Various bioinformatics problems require optimizing several different properties simultaneously. For example, in the protein threading problem, a linear scoring function combines the values for different properties of possible sequence-to-structure alignments into a single score to allow for unambigous optimization. In this context, an essential question is how each property should be weighted. As the native structures are known for some sequences, the implied partial ordering on optimal alignments may be used to adjust the weights. To resolve the arising interdependence of weights and computed solutions, we propose a novel approach: iterating the computation of solutions (here: threading alignments) given the weights and the estimation of optimal weights of the scoring function given these solutions via a systematic calibration method. We show that this procedure converges to structurally meaningful weights, that also lead to significantly improved performance on comprehensive test data sets as measured in different ways. The latter indicates that the performance of threading can be improved in general.

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Parallelization of a 3D magnetostatic code using High Performance Fortran

Parallelization of a 3D magnetostatic code using High Perfor...

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International Conference on Parallel computing in Electrical Engineering (PARLEC)

作者： E. Cagniot J.L. Dekeyser P. Boulet T. Brandes F. Piriou G. Marques Laboratoire dhformatique Fondamentale de Lille (LIFL) USTL-Cité scientifique Villeneuve d'Ascq France Institute for Algorithms and Scientific Computing (SCAI) German National Research Center for Information Technology (GMD) Augustin Germany Laboratoire d Electrotechnique et dElectronique de Puissance (L2EP) USTL-Cité scientifique Villeneuve d'Ascq France

Numerical simulation in electrical engineering allows one to reduce development costs by predicting device performance. An accurate prediction often requires 3D models, inducing high storage capacity and CPU power needs. As computation times can be very important, parallel computers are well suited to these models. 3D simulation in electrical engineering is based on recent research work (Whitney's elements, auto-gauged formulations, discretization of the source terms) and it results in complex and irregular codes using sparse matrices, where data accesses are done via indirect addressing. We present the results of the parallelization of a 3D magnetostatic code using High Performance Fortran (HPF). This high level programming language allows a simple and efficient approach to parallel machines. It provides both easier maintenance of the code and higher software productivity for electrical engineers.

关键词： Magnetostatics Electrical engineering Concurrent computing Power engineering computing Numerical simulation Costs Predictive models Central Processing Unit Computational modeling Computer simulation

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FETI and Neumann-Neumann iterative substructuring methods: Connections and new results

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Communications on Pure and Applied Mathematics 2000年第1期54卷

作者： Axel Klawonn Olof Widlund GMD—German National Research Center for Information Technology SCAI—Institute for Algorithms and Scientific Computing Schloss Birlinghoven D-53754 Sankt Augustin Germany Courant Institute 251 Mercer Street New York NY 10012

The FETI and Neumann-Neumann families of algorithms are among the best known and most severely tested domain decomposition methods for elliptic partial differential equations. They are iterative substructuring methods and have many algorithmic components in common, but there are also differences. The purpose of this paper is to further unify the theory for these two families of methods and to introduce a new family of FETI algorithms. Bounds on the rate of convergence, which are uniform with respect to the coefficients of a family of elliptic problems with heterogeneous coefficients, are established for these new algorithms. The theory for a variant of the Neumann-Neumann algorithm is also redeveloped stressing similarities to that for the FETI methods. © 2001 John Wiley & Sons, Inc.

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Docking of hydrophobic ligands with interaction-based matching algorithms

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BIOINFORMATICS 1999年第3期15卷 243-250页

作者： Rarey, M Kramer, B Lengauer, T German National Research Center for Information Technology (GMD) Institute for Algorithms and Scientific Computing (SCAI) Schloss Birlinghoven 53754 Sankt Augustin Germany. Rarey@gmd.de

Motivation: Matching of chemical interacting groups is a common concept for docking and fragment placement algorithms in computer-aided drug design. These algorithms have been proven to be reliable and fast if at least a certain number of hydrogen bonds or salt bridges occur: However, the algorithms typically run into problems if hydrophobic fragments or ligands should be placed In order to dock hydrophobic fragments without significant loss of computational efficiency we have extended the interaction model and placement algorithms in our docking tool FlexX. The concept of multi-level interactions is introduced into the algorithms for automatic selection and placement of base fragments. Results: With the multi-level interaction model and the corresponding algorithmic extensions, we were able to improve the overall performance of FlexX significantly. We tested the approach with a set of 200 protein-ligand complexes taken from the Brookhaven Protein Data Bank (PDB). The number of test cases which can be docked within 1.5 Angstrom RMSD from the crystal structure can be increased from 58 to 64%. The performance gain is paid for by an increase in computation time from 73 to 91 s on average per protein-ligand complex.

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Contribution to better handling of irregular problems in HPF2

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4th International Conference on Parallel Processing, Euro-Par 1998

作者： Brandes, Thomas Brégier, Frédéric Counilh, Marie Christine Roman, Jean GMD/SCAI Institute for Algorithms and Scientific Computing German National Research Center for Computer Science Schloss Birlinghoven 53754 St. Augustin Germany LaBRI ENSERB Université Bordeaux i 33405 Talence Cedex France

ISBN: (纸本)3540649522

In this paper, we present our contribution for handling irregular applications with HPF2. We propose a programming style of irregular applications close to the regular case, so that both compile-time and run-time techniques can be more easily performed. We use the well-known tree data structure to represent irregular data structures with hierarchical access, such as sparse matrices. This algorithmic representation avoids the indirections coming from the standard irregular programming style. We use derived data types of Fortran 90 to define trees and some approved extensions of HPF2 for their mapping. We also propose a run-time support for irregular applications with loop-carried dependencies that cannot be determined at compile-time. Then, we present the TriDenT library, which supports distributed trees and provides runtime optimizations based on the inspector/executor paradigm. Finally, we validate our contribution with experimental results on IBM SP2 for a sparse Cholesky factorization algorithm.

关键词： Trees (mathematics)

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CASP2 experiences with docking flexible ligands using FLEXX†

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Proteins: Structure, Function, and Bioinformatics 1998年第S1期29卷

作者： Bernd Kramer Matthias Rarey Thomas Lengauer German National Research Center for Information Technology (GMD) Institute for Algorithms and Scientific Computing (SCAI) Schloß Birlinghoven Germany

We have applied our docking program FLEXX to all eight CASP2 targets involving protein complexes with small ligands. Of the seven targets that were kept in the CASP2 experiment, we could solve two. We found important parts of the solution in four other examples, and were unsuccessful on the remaining example. This paper discusses all predictions in detail. Each of our prediction runs took just a few minutes of computer time on a standard workstation and could thus be demonstrated in real time at the CASP meeting. We believe that this speed is the prime strength of our program FLEXX. In quality, our predictions are competitive with those produced by other predictors. The experiment showed that possible objectives of improvement of the FLEXX program are to incorporate relevant aspects of receptor flexibility, deal with water molecules in the receptor pocket, allow for a postoptimization to refine favorable complexes, and improve the scoring function. Proteins, Suppl. 1:221–225, 1997. © 1998 Wiley-Liss, Inc.

关键词： molecular docking flexible docking protein–ligand interaction molecular flexibility conformational analysis drug design

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