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Confidence measures for protein fold recognition

BIOINFORMATICS 2002年第6期18卷 802-812页

作者： Sommer, I Zien, A von Öhsen, N Zimmer, R Lengauer, T Fraunhofer Inst Algorithms & Sci Comp D-53754 St Augustin Germany

Motivation: We present an extensive evaluation of different methods and criteria to detect remote homologs of a given protein sequence. We investigate two associated problems: first, to develop a sensitive searching method to identify possible candidates and, second, to assign a confidence to the putative candidates in order to select the best one. For searching methods where the score distributions are known, p-values are used as confidence measure with great success. For the cases where such theoretical backing is absent, we propose empirical approximations to p-values for searching procedures. Results: As a baseline, we review the performances of different methods for detecting remote protein folds (sequence alignment and threading, with and without sequence profiles, global and local). The analysis is performed on a large representative set of protein structures. For fold recognition, we find that methods using sequence profiles generally perform better than methods using plain sequences, and that threading methods perform better than sequence alignment methods. In order to assess the quality of the predictions made, we establish and compare several confidence measures, including raw scores, Z-scores, raw score gaps, z-score gaps, and different methods of p-value estimation. We work our way from the theoretically well backed local scores towards more explorative global and threading scores. The methods for assessing the statistical significance of predictions are compared using specificity-sensitivity plots. For local alignment techniques we find that p-value methods work best, albeit computationally cheaper methods such as those based on score gaps achieve similar performance. For global methods where no theory is available methods based on score gaps work best. By using the score gap functions as the measure of confidence we improve the more powerful fold recognition methods for which p-values are unavailable.

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Soft document clustering using a novel graph covering approach

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BIODATA MINING 2018年第1期11卷 1-20页

作者： Doerpinghaus, Jens Schaaf, Sebastian Jacobs, Marc Fraunhofer Inst Algorithms & Sci Comp Schloss Birlinghoven Sankt Augustin Germany

Background: In text mining, document clustering describes the efforts to assign unstructured documents to clusters, which in turn usually refer to topics. Clustering is widely used in science for data retrieval and organisation. Results: In this paper we present and discuss a novel graph-theoretical approach for document clustering and its application on a real-world data set. We will show that the well-known graph partition to stable sets or cliques can be generalized to pseudostable sets or pseudocliques. This allows to perform a soft clustering as well as a hard clustering. The software is freely available on GitHub. Conclusions: The presented integer linear programming as well as the greedy approach for this NP-complete problem lead to valuable results on random instances and some real-world data for different similarity measures. We could show that PS-Document Clustering is a remarkable approach to document clustering and opens the complete toolbox of graph theory to this field.

关键词： Document clustering Information retrieval Graph theory

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Wolf₂Pack - Portal Based Atomistic Force-Field Development

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JOURNAL OF CHEMICAL INFORMATION AND MODELING 2013年第4期53卷 802-808页

作者： Kraemer-Fuhrmann, Ottmar Neisius, Jens Gehlen, Niklas Reith, Dirk Kirschner, Karl N. Fraunhofer Inst Algorithms & Sci Comp Dept Simulat Engn D-53754 Schloss Birlinghoven Sankt Augustin Germany Fraunhofer Inst Algorithms & Sci Comp Dept Bioinformat D-53754 Schloss Birlinghoven Sankt Augustin Germany

In this contribution we introduce the technical concept and implementation details concerning the front end of our force-field optimization workflow package for intramolecular degrees of freedom, called Wolf(2)Pack. The package's design follows our belief that parameter optimization should be a user-driven, but program guided, workflow with specific modular tasks that reduce human errors and save time. Through this design, parameter optimization becomes more reliable and reproducible. Wolf(2)Pack can integrate common force fields from different research areas, allowing the user to optimize balanced parameters;alternatively users can develop highly specialized force fields that suite their chemical systems. Included in the package's front end is a force-field and molecular database whose contents facilitate parameter optimization. Wolf2Pack can be accessed at ***.

关键词： Optimization Molecular mechanics Chemical calculations Molecules Biological databases

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Petri and how he saw the world

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SOFTWARE AND SYSTEMS MODELING 2015年第2期14卷 727-733页

作者： Smith, Einar Fraunhofer Inst Algorithms & Sci Comp SCAI Schloss Birlinghoven D-53754 St Augustin Germany

This article is a short summary and explanation of the scientific work of Carl Adam Petri. The very basics of net theory are sufficient to understand it.

关键词： Petri Nets Concurrency Asynchronous systems Discrete density Measuring theory

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Decomposition of ordinary differential equations

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BULLETIN OF MATHEMATICAL sciENCES 2017年第3期7卷 575-613页

作者： Schwarz, Fritz Fraunhofer Inst Algorithms & Sci Comp SCAI D-53754 St Augustin Germany

Decompositions of linear ordinary differential equations (ode's) into components of lower order have successfully been employed for determining their solutions. Here this approach is generalized to nonlinear ode's. It is not based on the existence of Lie symmetries, in that it is a genuine extension of the usual solution algorithms. If an equation allows a Lie symmetry, the proposed decompositions are usually more efficient and often lead to simpler expressions for the solution. For the vast majority of equations without a Lie symmetry decomposition is the only available systematic solution procedure. Criteria for the existence of diverse decomposition types and algorithms for applying them are discussed in detail and many examples are given. The collection of Kamke of solved equations, and a tremendeous compilation of random equations are applied as a benchmark test for comparison of various solution procedures. Extensions of these proceedings for more general types of ode's and also partial differential equations are suggested.

关键词： Ordinary differential equations Decomposition Exact solutions

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Flexible docking under pharmacophore type constraints

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JOURNAL OF compUTER-AIDED MOLECULAR DESIGN 2002年第2期16卷 129-149页

作者： Hindle, SA Rarey, M Buning, C Lengauer, T Fraunhofer Inst Algorithms & Sci Comp FhI SCAI Schloss Birlinghoven D-53754 St Augustin Germany

FlexX-Pharm, an extended version of the flexible docking tool FlexX, allows the incorporation of information about important characteristics of protein-ligand binding modes into a docking calculation. This information is introduced as a simple set of constraints derived from receptor-based type pharmacophore features. The constraints are determined by selected FlexX interactions and inclusion volumes in the receptor active site. They guide the docking process to produce a set of docking solutions with particular properties. By applying a series of look-ahead checks during the flexible construction of ligand fragments within the active site, FlexX-Pharm determines which partially built docking solutions can potentially obey the constraints. Solutions that will not obey the constraints are deleted as early as possible, often decreasing the calculation time and enabling new docking solutions to emerge. FlexX-Pharm was evaluated on various individual protein-ligand complexes where the top docking solutions generated by FlexX had high root mean square deviations (RMSD) from the experimentally observed binding modes. FlexX-Pharm showed an improvement in the RMSD of the top solutions in most cases, along with a reduction in run time. We also tested FlexX-Pharm as a database screening tool on a small dataset of molecules for three target proteins. In two cases, FlexX-Pharm missed one or two of the active molecules due to the constraints selected. However, in general FlexX-Pharm maintained or improved the enrichment shown with FlexX, while completing the screen in considerably less run time.

关键词： constraint flexible docking molecular modeling pharmacophore protein-ligand interaction virtual screening

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Quasi-Monte Carlo and RBF Metamodeling for Quantile Estimation in River Bed Morphodynamics 3

Quasi-Monte Carlo and RBF Metamodeling for Quantile Estimati...

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3rd International Conference on Simulation and Modeling Methodologies, Technologies and Applications (SIMULTECH)

作者： Clees, Tanja Nikitin, Igor Nikitina, Lialia Pott, Sabine Fraunhofer Inst Algorithms & Sci Comp St Augustin Germany

ISBN: (纸本)9783319114569

Four generic methods for quantile estimation have been compared: Monte Carlo (MC), Monte Carlo with Harrel-Davis weighting (WMC), quasi-Monte Carlo with Sobol sequence (QMC) and quasi-random splines (QRS). The methods are combined with RBF metamodel and applied to the analysis of morphodynamic-hydrodynamic simulations of the river bed evolution. The following results have been obtained. Harrel-Davis weighting gives a moderate 10-20 % improvement of precision at small number of samples N similar to 100. Quasi-Monte Carlo methods provide significant improvement of quantile precision, e.g. the number of function evaluations necessary to achieve rms similar to 10(-4) precision is reduced from 1,000,000 for MC to 100,000 for QMC and to 6,000 for QRS. On the other hand, RBF metamodeling of bulky data allows to speed up the computation of one complete result in the considered problem from 45 min (on 32CPU) to 20 s (on 1CPU), providing rapid quantile estimation for the whole set of bulky data.

关键词： Stochastic analysis Response surfaces Fluid dynamics simulation

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Towards interactive simulation in automotive design

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VISUAL compUTER 2008年第11期24卷 947-953页

作者： Stork, Andre Thole, Clemens-August Klimenko, Stanislav Nikitin, Igor Nikitina, Lialia Astakhov, Yuri SCAI Fraunhofer Inst Algorithms & Sci Comp St Augustin Germany IGD Fraunhofer Inst Comp Graph Darmstadt Germany ICPT Inst Comp Phys & Technol Moscow Russia Univ Cologne Inst Math D-5000 Cologne Germany

One of the important tasks in Mechanical Engineering is to increase the safety of the vehicle and decrease its production costs. This task is typically solved by means of Multiobjective Optimization, which formulates the problem as a mapping from the space of design variables to the space of target criteria and tries to find an optimal region in these multidimensional spaces. Due to high computational costs of numerical simulations, the sampling of this mapping is usually very sparse and scattered. Combining design of experiments methods, metamodeling, new interpolation schemes and innovative graphics methods, we enable the user to interact with simulation parameters, optimization criteria, and come to a new interpolated crash result within seconds. We denote this approach as Simulated Reality, a new concept for the interplay between simulation, optimization and interactive visualization. In this paper we show the application of Simulated Reality for solution of real life car design optimization problems.

关键词： Simulation Optimization Progressive meshes Virtual production engineering

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Document Clustering using a Graph Covering with Pseudostable Sets

Document Clustering using a Graph Covering with Pseudostable...

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Federated Conference on computer science and Information Systems (FedCSIS)

作者： Doerpinghaus, Jens Schaaf, Sebastian Fluck, Juliane Jacobs, Marc Schloss Birlinghoven Fraunhofer Inst Algorithms & Sci Comp St Augustin Germany

ISBN: (纸本)9788394625375

In text mining, document clustering describes the efforts to assign unstructured documents to clusters, which in turn usually refer to topics. Clustering is widely used in science for data retrieval and organisation. In this paper we present a new graph theoretical approach to document clustering and its application on a real-world data set. We will show that the well-known graph partition to stable sets or cliques can be generalized to pseudostable sets or pseudocliques. This allows to make a soft clustering as well as a hard clustering. We will present an integer linear programming and a greedy approach for this NP-complete problem and discuss some results on random instances and some real world data for different similarity measures.

关键词： Color Minimization Clustering algorithms Integer linear programming Graph theory Optimization Manganese

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What was the Question? A Systematization of Information Retrieval and NLP Problems

What was the Question? A Systematization of Information Retr...

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Federated Conference on computer science and Information Systems (FedCSIS)

作者： Doerpinghaus, Jens Darms, Johannes Jacobs, Marc Fraunhofer Inst Algorithms & Sci Comp Schloss Birlinghoven Sankt Augustin Germany

ISBN: (纸本)9788394941956

In this paper we suggest novel systematization of Information Retrieval and Natural Language Processing problems. Using this rather general description of problems we are able to discuss and proof the equivalence of some problems. We provide reformulations of well-known problems like Named Entity Recognition using our novel description and discuss further research and the expected outcome. We will discuss the relation of two problems, cluster labeling and search query finding. With these results we are able to provide a novel optimization approach to both problems. This novel systematization approach provides a yet unknown view generating new classes of problems in NLP. It brings application and algorithmic approaches together and offers a better description with concepts of theoretical computer science.

关键词： Natural language processing systems

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