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Time-efficient flexible superposition of medium-sized molecules

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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Quantifying the local reliability of a sequence alignment

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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

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

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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

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Computational methods for biomolecular docking

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CURRENT OPINION IN STRUCTURAL BIOLOGY 1996年第3期6卷 402-406页

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

With the rapidly increasing amount of molecular biological data available, the computer-based analysis of molecular interactions becomes more and more feasible. Methods for computer-aided molecular docking have to include a reasonably accurate model of energy and must be able to deal with the combinatorial complexity incurred by the molecular flexibility of the docking partners. In both respects, recent years have seen substantial progress.

关键词： Models Molecular Protein Binding Databases Factual Drug Design Research Support Non-U.S. Gov't Software

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Adaptive parallel multigrid in computational fluid dynamics

Adaptive parallel multigrid in computational fluid dynamics

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Proceedings of the International Conference and Exhibition on High-Performance computing and Networking

作者： Wu, J. Institute for Algorithms and Scientific Computing (SCAI) GMD-German National Research Center for Information Technology SchloßBirlinghoven Sankt Augustin 53754 Germany

ISBN: (纸本)9783540611424

In this paper the numerical and parallel efficiency of the adaptive parallel strategy employed in a multigrid-solver package LiSS, developed in GMD-scai, are discussed. Two main aspects in these issues are adaptive criterion and data-redistribution concept for load balancing. The adaptive criterion is based on the finite-element-residuals of governing equations. It can find refinement regions automatically, e.g. near shocks and geometric singularities. For parallelization new data in the adaptive phase can be re-distributed by sub-dividing and remapping the sub-blocks onto exisiting processors to obtain approximate load balancing. The 2D exmaples of Euler equations and incompressible Navier- Stokes equations in this paper show obviously high numerical and parallel efficiency of LiSS. © Springer-Verlag Berlin Heidelberg 1996.

关键词： Navier Stokes equations

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An environment for the parallel solution of coupled problems on structured grids 3rd

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3rd International Workshop on Applied Parallel computing in Industrial Problems and Optimization, PARA 1996

作者： Hackenberg, Matthias G. Joppieh, Wolfgang Mijalković, Slobodan SCAI-Institute for Algorithms and Scientific Computing GMD-German National Research Center for Information Technology Sankt Augustin53754 Germany University of Niš Beogradska 14 Nig18000 Yemen

ISBN: (纸本)3540620958

The solution of coupled problems is one of the grand challenges in scientific computing. Many problems can only be solved partially. Not all dependencies can be taken into account, e.g. only subproblems can be solved completely, even when optimal numerical methods (multigrid methods) are used. Therefore, parallel simulation is inevitable. Coupled simulation of problems with different numerical complexities is possible now. An environment has been developed, which is an extension of LiSS (environment for the parallel multigrid solution of partial differential equations on general 2D domains). Block-structured grids with overlap are the basis for parallelization. In order to achieve acceptable load-balance each subproblem is distributed to all processors. Components of the multigrid algorithm can be selected separately for each subproblem, thus allowing optimal methods for each problem. In addition, a large number of coupling strategies can be used, varying from coupling after each time step to coupling after each relaxation. This strategy can be used in a real life example from VLSI wafer fabrication, where oxidation and diffusion are simulated coupled and in parallel. © Springer-Verlag Berlin Heidelberg 1996.

关键词： Numerical methods

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Coupling fluids and structures codes on MPI

Coupling fluids and structures codes on MPI

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Proceedings of the MPI Developer's Conference

作者： K. Wolf E. Brakkee GMD-German National Research Center for Computer Science SCAI-Institute for Algorithms and Scientific Computing Sankt Augustin Germany

In the last few years lots of industrial simulation applications were ported onto parallel systems to gain more computational power. Besides other parallelisation techniques message-passing seems to be the most powerful and accepted one. Since MPI is the upcoming standard definition for message-passing libraries, portability and adaptation among different hardware- and software-environments becomes more and more realistic. However some problems are still unsolved, if two or more independent parallel MPI-applications are coupled and work together. This article shows some of the problems which might arise in coupling independent parallel codes: e.g. management of separate address spaces, definition of dedicated neighborhoods, integration of dynamic process sets and synchronisation events.

关键词： Application software Software libraries Computer industry Computational modeling Automotive engineering Concurrent computing Vehicle dynamics Visualization Computer science scientific computing

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High performance C++

High performance C++

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International Conference and Exhibition on High-Performance computing and Networking

作者： Wolf, K Holtz, A Lang, M Institute for Algorithms and Scientific Computing (SCAI) German National Research Center for Computer Science (GMD) Schloss Birlinghoven Sankt Augustin D-53754 Germany

ISBN: (纸本)3540593934

HPC++ is a object-oriented programming environment dedicated to distributed memory parallel computers. It is based on a process model and integrates various parallel programming paradigms. Modularisation, interfaces and dynamic configuration are basic features. Parallel prototypes may be encapsulated in subnets. In the context of an existing commercial CASE tool HPC++ will be used as target language for the translation from graphical design method into code. Within one year, exploitation of HPC++ will be started offering an object-oriented library on top of standard parallel runtime systems.

关键词： Object oriented programming

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Computational Life Sciences 1

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丛书名： Studies in Big Data

1000年

作者： Jens Dörpinghaus Sebastian Schaaf Vera Weil Alexander Apke

ISBN: (数字)9783031084119

ISBN: (纸本)9783031084102;9783031084133

This book broadly covers the given spectrum of disciplines in Computational Life Sciences, transforming it into a strong helping hand for teachers, students, practitioners and researchers. In Life Sciences, problem-solving and data analysis often depend on biological expertise combined with technical skills in order to generate, manage and efficiently analyse big data. These technical skills can easily be enhanced by good theoretical foundations, developed from well-chosen practical examples and inspiring new strategies. This is the innovative approach of Computational Life Sciences-Data Engineering and Data Mining for Life Sciences: We present basic concepts, advanced topics and emerging technologies, introduce algorithm design and programming principles, address data mining and knowledge discovery as well as applications arising from real projects. Chapters are largely independent and often flanked by illustrative examples and practical advise.

关键词： Data Engineering Bioinformatics Big Data Computational Intelligence

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Carl Adam Petri 1

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1000年

作者： Einar Smith

ISBN: (数字)9783662480939

ISBN: (纸本)9783662480922;9783662516836

The book presents the life and works of one of Germany's most famous computer scientists, Carl Adam Petri. It is written in a vivid and entertaining manner, providing an in-depth discussion of the background behind Petri's best-known contribution to computer science, the Petri net. In this way the book can be read as a first introduction to nets, but it also covers the theoretical, physical and philosophical foundations behind nets, thus facilitating a comprehensive understanding of the wider range of Petri's works. The book is intended for readers with a previous knowledge in computer science, as well as for “interested non-professionals”, who want to get to know a remarkable personality of contemporary science.

关键词： History of computing Mathematics, general Philosophy, general Theory of Computation

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