检索结果-内蒙古大学图书馆

CASP2 experiences with docking flexible ligands using FLEXX†

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

来源：评论

学校读者我要写书评

暂无评论

ADAPTIVE PARALLEL MULTIGRID SOLUTION OF 2D INCOMPRESSIBLE NAVIER–STOKES EQUATIONS

引用

International Journal for Numerical Methods in Fluids 1998年第9期24卷

作者： Jian Wu Hubert Ritzdorf Kees Oosterlee Barbara Steckel Anton Schüller Institute of Algorithms and Scientific Computing GMD—German Research Centre for Information Technology Schloss Birlinghoven D-53754 Sankt Augustin Germany

In this paper an adaptive parallel multigrid method and an application example for the 2D incompressible Navier–Stokes equations are described. The strategy of the adaptivity in the sense of local grid refinement in the multigrid context is the multilevel adaptive technique (MLAT) suggested by Brandt. The parallelization of this method on scalable parallel systems is based on the portable communication library CLIC and the message-passing standards: PARMACS, PVM and MPI. The specific problem considered in this work is a two-dimensional hole pressure problem in which a Poiseuille channel flow is disturbed by a cavity on one side of the channel. Near geometric singularities a very fine grid is needed for obtaining an accurate solution of the pressure value. Two important issues of the efficiency of adaptive parallel multigrid algorithms, namely the data redistribution strategy and the refinement criterion, are discussed here. For approximate dynamic load balancing, new data in the adaptive steps are redistributed into distributed memories in different processors of the parallel system by block remapping. Among several refinement criteria tested in this work, the most suitable one for the specific problem is that based on finite-element residuals from the point of view of self-adaptivity and computational efficiency, since it is a kind of error indicator and can stop refinement algorithms in a natural way for a given tolerance. Comparisons between different global grids without and with local refinement have shown the advantages of the self-adaptive technique, as this can save computer memory and speed up the computing time several times without impairing the numerical accuracy. © 1997 By John Wiley & Sons, Ltd. Int. J. Numer. Methods Fluids 24, 875–892, 1997.

关键词： adaptive parallel multigrid method local refinement criteria incompressible Navier–Stokes equations hole pressure problem

来源：评论

学校读者我要写书评

暂无评论

Adaptive parallel multigrid solution of 2D incompressible Navier-Stokes equations

引用

INTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN FLUIDS 1997年第9期24卷 875-892页

作者： Wu, J Ritzdorf, H Oosterlee, K Steckel, B Schuller, A Institute of Algorithms and Scientific Computing GMD—German Research Centre for Information Technology Schloss Birlinghoven D-53754 Sankt Augustin Germany [*]Institute of Algorithms and Scientific Computing German Research Centre for Information Technology Schloss Birlinghoven D-53754 Sankt Augustin Germany

In this paper an adaptive parallel multigrid method and an application example for the 2D incompressible Navier-Stokes equations are described. The strategy of the adaptivity in the sense of local grid refinement in the multigrid context is the multilevel adaptive technique (MLAT) suggested by Brandt. The parallelization of this method on scalable parallel systems is based on the portable communication library CLIC and the message-passing standards: PARMACS, PVM and MPI. The specific problem considered in this work is a two-dimensional hole pressure problem in which a Poiseuille channel flow is disturbed by a cavity on one side of the channel. Near geometric singularities a very fine grid is needed for obtaining an accurate solution of the pressure value. Two important issues of the efficiency of adaptive parallel multigrid algorithms, namely the data redistribution strategy and the refinement criterion, are discussed here. For approximate dynamic load balancing, new data in the adaptive steps are redistributed into distributed memories in different processors of the parallel system by block remapping. Among several refinement criteria tested in this work, the most suitable one for the specific problem is that based on finite-element residuals from the point of view of self-adaptivity and computational efficiency, since it is a kind of error indicator and can stop refinement algorithms in a natural way for a given tolerance. Comparisons between different global grids without and with local refinement have shown the advantages of the self-adaptive technique, as this can save computer memory and speed up the computing time several times without impairing the numerical accuracy. (C) 1997 By John Wiley & Sons, Ltd.

关键词： adaptive parallel multigrid method local refinement criteria incompressible Navier-Stokes equations hole pressure problem

来源：评论

学校读者我要写书评

暂无评论

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

引用

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

来源：评论

学校读者我要写书评

暂无评论

Time-efficient flexible superposition of medium-sized molecules

引用

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

来源：评论

学校读者我要写书评

暂无评论

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

引用

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

来源：评论

学校读者我要写书评

暂无评论

Parallel 'Go with the winners' algorithms in the LogP model

Parallel 'Go with the winners' algorithms in the LogP model

引用

International Symposium on Parallel Processing

作者： M. Peinado T. Lengauer German National Research Center for Information Technology GMD Institute for Algorithms and Scientific Computing Sankt Augustin Germany

The authors parallelize the 'Go with the winners' algorithm of Aldous and Vazirani (1994) and analyze the resulting parallel algorithm in the LogP-model. The main issues in the analysis are load imbalances and communication delays. The result of the analysis is a practical algorithm which, under reasonable assumptions, achieves linear speedup. Finally, they analyze the algorithm for a concrete application: generating models of amorphous chemical structures.

关键词： Algorithm design and analysis Concrete Delay Chemical analysis Monte Carlo methods Approximation algorithms Polynomials Simulated annealing Information technology scientific computing

来源：评论

学校读者我要写书评

暂无评论

A CLASS OF MULTI-PARAMETER RELAXED PARALLEL MULTISPLITTING METHODS FOR LARGE SPARSE LINEAR COMPLEMENTARITY PROBLEMS

引用

Parallel algorithms and Applications. 1997年第1-2期11卷 113-127页

作者： ZHONG-ZHI BAI D. J. EVANS DE-REN WANG [a] State Key Laboratory of Scientific/Engineering Computing Institute of Computational Mathematics and Scientific/Engineering Computing Chinese Academy of Sciences Beijing P.R. China [b] Parallel Algorithms Research Centre Loughborough University of Technology Loughborough Leicestershire LE11 3TU U.K England U.K. [c] Department of Mathematics Shanghai University (Jiading Campus) Shanghai 201800 P.R China

We set up a class of multi-parameter relaxed parallel matrix multisplitting methods for solving the linear complementarity problems on the SIMD multiprocessor systems. This class of methods can not only includes all the existing relaxed methods for the linear complementarity problems, but also can yields a lot of novel ones in the sense of multisplitting. Thus, it is reasonably general. We set up the convergence theory of these relaxed methods under the condition that the system matrix is an H-matrix with positive diagonal elements.

关键词： linear complementarity problem matrix multisplitting relaxation method convergence theory H-matrix

来源：评论

学校读者我要写书评

暂无评论

Flux difference splitting for three-dimensional steady incompressible Navier-Stokes equations in curvilinear co-ordinates

引用

INTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN FLUIDS 1996年第4期23卷 347-366页

作者： Oosterlee, CW Ritzdorf, H German National Research Center for Information Technology Institute for Algorithms and Scientific Computing (GMD SCAI) Schloss Birlinghoven D-53754 St. Augustin Germany

A collocated discretization of the 3D steady incompressible Navier-Stokes equations based on a flux-difference-splitting formulation is presented. The discretization employs primitive variables of Cartesian velocity components and pressure. The splitting used here is a polynomial splitting introduced by Dick and Linden of Roe type. Second-order accuracy is obtained with the defect correction approach in which the state vector is interpolated with van Leer's K-scheme. The underlying solution technique to solve the discretized equations is a parallel multiblock multigrid method. Several 2D and 3D test problems such as driven cavity and channel flows are solved.

关键词： three-dimensional incompressible Navier-Stokes collocated grid curvilinear co-ordinates flux difference splitting defect correction multigrid

来源：评论

学校读者我要写书评

暂无评论

Quantifying the local reliability of a sequence alignment

引用

PROTEIN ENGINEERING 1996年第2期9卷 127-132页

作者： Mevissen, HT Vingron, M German National Research Center for Computer Science (GMD) Institute for Algorithms and Scientific Computing (SCAI) SchlossBirlinghoven D-53754 St Augustin Germany

We present a method for attributing a measure of reliability to a residue pair in an optimal alignment of two protein sequences. Validation based on a database of structurally correct alignments [Pascarella and Argos (1992) Protein Engng, 5, 121-137] shows that correctly aligned parts of a sequence alignment systematically receive high scores in this measure, The higher the sequence similarity between two sequences, the larger is the fraction found of the correct parts of the alignment, We used these observations to design a program that draws a reliability curve along an optimal alignment reflecting the chances for each residue pair to be aligned correctly.

关键词： alignment reliability protein sequence alignment

来源：评论

学校读者我要写书评

暂无评论

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案：

请选择收藏分类：

通借通还

建议与咨询 留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案： 新增检索档案 确定 取消

请选择收藏分类： 新增自定义分类 确定 取消

通借通还

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

请选择保存的检索档案：

请选择收藏分类：