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

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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Multiple automatic base selection: Protein-ligand docking based on incremental construction without manual intervention

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JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN 1997年第4期11卷 369-384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 D-53754 Sankt Augustin Germany German National Research Center for Information Technology (gmd) Institute for Algorithms and Scientific Computing (SCAI) Schloss Birlinghoven D-53754 Sankt Augustin Germany German National Research Center for Information Technology (gmd) Institute for Algorithms and Scientific Computing (SCAI) Schloss Birlinghoven D-53754 Sankt Augustin Germany

A possible way of tackling the molecular docking problem arising in computer-aided drug design is the use of the incremental construction method. This method consists of three steps: the selection of a part of a molecule a so-called base fragment, the placement of the base fragment into the active site of a protein, and the subsequent reconstruction of the complete drug molecule. Assuming that a part of a drug molecule is known, which is specific enough to be a good base fragment,the method is proven to be successful for a large set of docking examples. In addition, it leads to the fastest algorithms for flexible docking published so far. In most real-world applications of docking, large sets of ligands have to be tested for affinity to a given protein. Thus, manual selection of a base fragment is not practical. On the other hand, the selection of a base fragment is critical in that only few selections lead to a low-energy structure. We overcome this limitation by selecting a representative set of base fragments instead of a single one. In this paper, we present a set of rules and algorithms to automate this selection. In addition, we extend the incremental construction method to deal with multiple fragmentations of the drug molecule. Our results show that with multiple automated base selection, the quality of the docking predictions is almost as good as with one manually preselected base fragment. In addition, the set of solutions is more diverse and alternative binding modes with low scores are found. Although the run time of the overall algorithm increases, the method remains fast enough to search through large ligand data sets.

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

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A GMRES-based plane smoother in multigrid to solve 3D anisotropic fluid flow problems

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JOURNAL OF COMPUTATIONAL PHYSICS 1997年第1期130卷 41-53页

作者： Oosterlee, CW German National Research Center for Information Technology Institute for Algorithms Scientific Computing (SCAI) Schloss Birlinghoven 53754 Sankt Augustin Germany

For a discretization of the 3D steady incompressible Navier-Stokes equations a solution method is presented for solving flow problems on stretched grids. The discretization is a vertex-centered finite volume discretization with a flux splitting approach for the convective terms. Second-order accuracy is obtained with the well-known defect correction technique (B. Koren, J. Comput Phys. 87, 25, 1990). The solution method used is multigrid, for which a plane smoother is presented for obtaining good convergence in flow domains with severely stretched grids. A matrix is set up in a plane, which is solved iteratively with a preconditioned GMRES method. Here, a stop criterion for GMRES is tested, which reduces the number of inner iterations compared to an ''exact'' plane solver without affecting the multigrid convergence rates. The performance of the solution method is shown for a Poisson model problem and for 3D incompressible channel flow examples. (C) 1997 Academic Press

关键词： Finite volume method

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Time-efficient flexible superposition of medium-sized molecules

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JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN 1997年第4期11卷 357-368页

作者： Lemmen, C Lengauer, T German National Research Center for Information Technology (gmd) Institute for Algorithms and Scientific Computing (SCAI) Schloss Birlinghoven D-53754 Sankt Augustin Germany German National Research Center for Information Technology (gmd) Institute for Algorithms and Scientific Computing (SCAI) Schloss Birlinghoven D-53754 Sankt Augustin Germany

We present an efficient algorithm for the structural alignment of medium-sized organic molecules. The algorithm has been developed for applications in 3D QSAR and in receptor modeling. The method assumes one of the molecules, the reference ligand, to be presented in the conformation that it adopts inside the receptor pocket. The second molecule, the test ligand, is considered to be flexible, and is assumed to be given in an arbitrary low-energy conformation. Ligand flexibility is modeled by decomposing the test ligand into molecular fragments, such that ring systems are completely contained in a single fragment. Conformations of fragments and torsional angles of single bonds are taken from a small finite set, which depends on the fragment and bond, respectively. The algorithm superimposes a distinguished base fragment of the test ligand onto a suitable region of the reference ligand and then attaches the remaining fragments of the test ligand in a step-by-step fashion. During this process, a scoring function is optimized that encompasses bonding terms and terms accounting for steric overlap as well as for similarity of chemical properties of both ligands. The algorithm has been implemented in the FLEXS system. To validate the quality of the produced results, we have selected a number of examples for which the mutual superposition of two ligands is experimentally given by the comparison of the binding geometries known from the crystal structures of their corresponding protein-ligand complexes. On more than two-thirds of the test examples the algorithm produces rms deviations of the predicted versus the observed conformation of the test ligand below 1.5 Angstrom. The run time of the algorithm on a single problem instance is a few minutes on a common-day workstation. The overall goal of this research is to drastically reduce run times, while limiting the inaccuracies of the model and the computation to a tolerable level.

关键词： structural alignment molecular superposition molecular similarity molecular flexibility drug design

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