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computational methods in protein structure prediction

BIOTECHNOLOGY AND BIOENGINEERING 2007年第2期97卷 207-213页

作者： Floudas, C. A. Princeton Univ Dept Chem Engn Princeton NJ 08544 USA

This review presents the advances in protein structure prediction from the computational methods perspective. The approaches are classified into four major categories: comparative modeling, fold recognition, first principles methods that employ database information, and first principles methods without database information. Important advances along with current limitations and challenges are presented.

关键词： protein structure prediction protein folding computational methods

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computational methods for recognition of cancer protein markers in saliva

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MATHEMATICAL BIOSCIENCES AND ENGINEERING 2020年第3期17卷 2453-2469页

作者： Sun, Ying Du, Wei Yang, Lili Dai, Min Dou, Ziying Wang, Yuxiang Liu, Jining Zheng, Gang Tianjin Univ Technol Sch Comp Sci & Engn Tianjin Key Lab Intelligence Comp & Novel Softwar Tianjin 300384 Peoples R China Civil Aviat Univ China Informat Technol Res Base Civil Aviat Adm China Tianjin 300300 Peoples R China Jilin Univ Coll Comp Sci & Technol Key Lab Symbol Computat & Knowledge Engn Minist Educ Changchun 130012 Peoples R China First Hosp Jilin Univ Dept Obstet Changchun 130012 Peoples R China

In recent years, many studies have supported that cancer tissues can make disease-specific changes in some salivary proteins through some mediators in the pathogenesis of systemic diseases. These salivary proteins have the potential to become cancer-specific biomarkers in the early diagnosis stage. How to effectively identify these potential markers is one of the challenging issues. In this paper, we propose novel machine learning methods for recognition cancer biomarkers in saliva by two stages. In the first stage, salivary secreted proteins are recognized which are considered as candidate biomarkers of cancers. We picked up 557 salivary secretory proteins from 20379 human proteins by public databases and published literatures. Then, we present a training set construction strategy to solve the imbalance problem in order to make the classification methods get better accuracy. From all human protein set, the proteins belonging to the same families as salivary secretory proteins are removed. After that, we use SVC-KM method to cluster the remaining proteins, and select negative samples from each cluster in proportion. Next, the features of proteins are calculated by tools. We collect 24 protein properties such as sequence, structure and physicochemical properties, a total of 1087 features. An innovative procedure based on the local samples is proposed for selecting the appropriate features, in order to further improve the performance of SVM classifier. Experimental results show that the average sensitivity, specificity and accuracy of salivary secretory protein recognition using selected 32 features in training set are 97.09%, 98.10%, 97.61%, respectively. The use of these methods can improve the accuracy of recognition by solving the problems of unbalanced sample size and uneven distribution in training set. In the second stage, we apply the best model to dig out the salivary secreted proteins from 58 reported cancer markers, and get a total of 42 proteins which are

关键词： salivary secretory protein cancer biomarker feature selection based on local samples SVC-KM computational methods

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computational methods in portfolio insurance

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APPLIED MATHEMATICS AND COMPUTATION 2007年第1期189卷 9-22页

作者： Katsikis, Vasilios N. Natl Tech Univ Athens Dept Math GR-15780 Athens Greece TEI Chalkis Dept Appl Sci GR-34400 Psahna Greece

In this article we develop a computational method for an algorithmic process first posed by Abramovich-Aliprantis-Polyrakis in 1994 in order to check whether a finite collection of linearly independent positive vectors in R-m forms a lattice-subspace. Lattice-subspaces are closely related to a cost minimization problem in the theory of finance that ensures the minimum-cost insured portfolio and this connection is further investigated here. Finally, we propose a computational method in order to solve the minimization problem and to calculate the minimum-cost insured portfolio. All of the numerical work is performed using the Matlab high-level language. (c) 2006 Elsevier Inc. All rights reserved.

关键词： matlab computational methods portfolio insurance lattice-subspaces positive basis

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computational methods for the structural alignment of molecules

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JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN 2000年第3期14卷 215-232页

作者： Lemmen, C Lengauer, T German Natl Res Ctr Informat Technol Inst Algorithms & Sci Comp D-53754 St Augustin Germany

In drug design, often enough, no structural information on a particular receptor protein is available. However, frequently a considerable number of different ligands is known together with their measured binding affinities towards a receptor under consideration. In such a situation, a set of plausible relative superpositions of different ligands, hopefully approximating their putative binding geometry, is usually the method of choice for preparing data for the subsequent application of 3D methods that analyze the similarity or diversity of the ligands. Examples are 3D-QSAR studies, pharmacophore elucidation, and receptor modeling. An aggravating fact is that ligands are usually quite flexible and a rigorous analysis has to incorporate molecular flexibility. We review the past six years of scientific publishing on molecular superposition. Our focus lies on automatic procedures to be performed on arbitrary molecular structures. Methodical aspects are our main concern here. Accordingly, plain application studies with few methodical elements are omitted in this presentation. While this review cannot mention every contribution to this actively developing field, we intend to provide pointers to the recent literature providing important contributions to computational methods for the structural alignment of molecules. Finally we provide a perspective on how superposition methods can effectively be used for the purpose of virtual database screening. In our opinion it is the ultimate goal to detect analogues in structure databases of nontrivial size in order to narrow down the search space for subsequent experiments.

关键词： computational methods review structural alignment

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computational methods for ultrasonic bone assessment

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ULTRASOUND IN MEDICINE AND BIOLOGY 1999年第5期25卷 823-830页

作者： Luo, GM Kaufman, JJ Chiabrera, A Bianco, B Kinney, JH Haupt, D Ryaby, JT Siffert, RS CyberLog Inc New York NY 10012 USA NYU Med Ctr Dept Vet Affairs Med Ctr New York NY 10016 USA NYU Med Ctr Dept Rehabil Med New York NY 10016 USA Mt Sinai Sch Med Dept Orthoped New York NY USA Univ Genoa Dept Biophys & Elect Engn Genoa Italy Univ Calif Lawrence Livermore Natl Lab Dept Mat Sci Livermore CA USA OrthoLog Corp Tempe AZ USA

Ultrasound has been proposed as a means to noninvasively assess bone and, particularly, bone strength and fracture risk. Although there has been some success in this application, there is still much that is unknown regarding the propagation of ultrasound through bone. Because strength and fracture risk are a function of both bone mineral density and architectural structure, this study was carried out to examine how architecture and density interact in ultrasound propagation. Due to the difficulties inherent in obtaining fresh bone specimens and associated architectural and density features, simulation methods were used to explore the interactions of ultrasound with bone. A sample of calcaneal trabecular bone was scanned with micro-CT and subjected to morphological image processing (erosions and dilations) operations to obtain a total of 15 three-dimensional (3-D) data sets. Fifteen two-dimensional (2-D) slices obtained from the 3-D data sets were then analyzed to evaluate their respective architectures and densities. The architecture was characterized through the fabric feature, and the density was represented in terms of the bone volume fraction. Computer simulations of ultrasonic propagation through each of the 15 2-D bone slices were carried out, and the ultrasonic velocity and mean frequency of the received waveforms were evaluated. Results demonstrate that ultrasound propagation is affected by both density and architecture, although there was not a simple linear correlation between the relative degree of structural anisotropy with the ultrasound measurements. This study elucidates further aspects of propagation of ultrasound through bone, and demonstrates as well as the power of computational methods for ultrasound research in general and tissue and bone characterization in particular. (C) 1999 World Federation for Ultrasound in Medicine & Biology.

关键词： computational methods ultrasound simulation trabecular bone bone mineral density architecture fabric ultrasound velocity mean frequency anisotropy

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computational methods for creep fracture analysis by damage mechanics

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COMPUTER methods IN APPLIED MECHANICS AND ENGINEERING 2000年第1-2期183卷 15-33页

作者： Murakami, S Liu, Y Mizuno, M Nagoya Univ Dept Mech Engn Chikusa Ku Nagoya Aichi 4648603 Japan Natl Res Council Canada Ctr Surface Transportat Technol Ottawa ON K1A 0R6 Canada

Some mechanical problems of the computational method of creep fracture analysis based on continuum damage mechanics are discussed. After brief review of the local approach to creep crack growth analysis by means of finite element analysis and continuum damage mechanics. intrinsic feature of the fracture analysis in the framework of continuum theory and the causes of mesh-dependence of the numerical results are discussed. Then, a series of numerical analyses are performed for a plate specimen with a central crack to show the characteristics of the mesh-dependence. In view of these results, the effects of stress-singularity at the crack tip as an essential cause of the mesh-dependence are discussed by analyzing the magnitude of stress in the finite element at the crack-tip. As another major cause of the mesh-dependence of the numerical results, ill-natured stress-sensitivity of the constitutive and the evolution equation of the conventional Kachanov-Rabotnov creep damage theory is elucidated by performing sensitivity analysis of the relevant equations. In order to suppress this singular stress sensitivity at the critical stage of damage, a new creep damage model is developed. Finally, the effects of the preceding damage held on stress singularity of the asymptotic stress field at mode I creep crack are analyzed to furnish a criterion to overcome the mesh-dependence in computational method for creep fracture analysis. (C) 2000 Elsevier Science S.A. All rights reserved.

关键词： computational methods

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computational methods for Traditional Chinese Medicine: A survey

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COMPUTER methods AND PROGRAMS IN BIOMEDICINE 2007年第3期88卷 283-294页

作者： Lukman, Suryani He, Yulan Hui, Siu-Cheung Univ Reading Informat Res Ctr Reading RG6 6BX Berks England Univ Cambridge Dept Chem Cambridge CB2 1EW England Nanyang Technol Univ Sch Comp Engn Singapore 639798 Singapore

Traditional Chinese Medicine (TCM) has been actively researched through various approaches, including computational techniques. A review on basic elements of TCM is provided to illuminate various challenges and progresses in its study using computational methods. Information on various TCM formulations, in particular resources on databases of TCM formulations and their integration to Western medicine, are analyzed in several facets, such as TCM classifications, types of databases, and mining tools. Aspects of computational TCM diagnosis, namely inspection, auscultation, pulse analysis as well as TCM expert systems are reviewed in term of their benefits and drawbacks. Various approaches on exploring relationships among TCM components and finding genes/proteins relating to TCM symptom complex are also studied. This survey provides a summary on the advance of computational approaches for TCM and will be useful for future knowledge discovery in this area. (C) 2007 Elsevier Ireland Ltd. All rights reserved.

关键词： computational methods Traditional Chinese Medicine data and text mining knowledge discovery survey

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computational methods for performance evaluation of a statistical multiplexer supporting bursty traffic

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IEEE-ACM TRANSACTIONS ON NETWORKING 1996年第3期4卷 386-397页

作者： Wu, GL Mark, JW UNIV WATERLOO DEPT ELECT & COMP ENGNWATERLOOON N2L 3G1CANADA

A statistical multiplexer supporting a number of bursty sources is modeled as a discrete time, single server queueing system with an infinite buffer. The probability generating function (PGF) method is used to analyze the queueing behavior. The PGF method requires the determination of a large number of boundary values and, hence, the roots of the characteristic equation. An iterative algorithm to evaluate the characteristic roots is proposed. When the arrival process is a superposition of independent processes, a decomposition approach is used to reduce the state space involved in the computational algorithm. Additionally, the computational algorithm is made efficient through the establishment of conditions under which all the roots are either real or nonnegative real numbers. A set of equations to recursively compute the moments of the queue length are established. Sample applications of the computational methods to evaluate the performance of a multiplexer supporting voice and video sources, modeled by two-state Markov and L-state MMPP processes, respectively, demonstrate the viability of the proposed methods.

关键词： Multiplexing Queueing Theory Discrete Time Systems Probability Iterative methods State Space methods Recursive Functions computational Complexity Markov Processes Stochastic Processes Visual Communication Telecommunication Traffic computational methods Performance Evaluation Statistical Multiplexer Bursty Traffic Bursty Sources Discrete Time Single Server Queueing System Infinite Buffer Probability Generating Function Method Boundary Values Characteristic Equation Iterative Algorithm Arrival Process Decomposition Approach State Space computational Algorithm Queue Length Moments Recursive Method Voice Source Video Source Two State Markov Processes L State MMPP Processes Markov Modulated Poisson Process Multiplexing Iterative Algorithms Aggregates Quantum Computing Probability Streaming Media Traffic Control computational Complexity Poisson Equations Queueing Analysis

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computational methods for investigating organic radical species

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ORGANIC & BIOMOLECULAR CHEMISTRY 2024年第30期22卷 6166-6173页

作者： Renningholtz, Tim Lim, Ethan R. X. James, Michael J. Trujillo, Cristina Univ Manchester Oxford Rd Manchester M13 9PL England Univ Dublin Trinity Coll Sch Chem TBSI Dublin D02 R590 Ireland

computational analysis of organic radical species presents significant challenges. This study compares the efficacy of various DFT and wavefunction methods in predicting radical stabilisation energies, bond dissociation energies, and redox potentials for organic radicals. The hybrid meta-GGA M062X-D3(0), and the range-separated hybrids omega B97M-V and omega B97M-D3(BJ) emerged as the most reliable functionals, consistently providing accurate predictions across different basis sets including 6-311G**, cc-pVTZ, and def2-TZVP. computational analysis of organic radical species presents significant challenges. This study compares the efficacy of various DFT and wavefunction methods in predicting radical stabilisation energies, bond dissociation energies, and redox potentials.

关键词： computational methods

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computational methods for Distributed Control of Heterogeneous Cyclic Interconnection Structures

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IEEE TRANSACTIONS ON AUTOMATIC CONTROL 2013年第8期58卷 2136-2142页

作者： Rice, Justin K. van Wingerden, Jan-Willem Delft Univ Technol Delft Ctr Syst & Control NL-2628 CD Delft Netherlands

We address the problem of fast system analysis and controller synthesis for heterogeneous subsystems interconnected in a loop. Such distributed systems have state-space realizations with a special matrix structure, which we show to be a generalization of the Sequentially Semi-Separable (SSS) structure employed in recent research on systems interconnected in a Cartesian array. By extending the O(N) structure-preserving SSS arithmetic to the matrices induced by this circular type of interconnection, we introduce a new cyclic SSS matrix structure and arithmetic which leads to fast and efficient procedures for linear computational complexity optimal distributed controller synthesis for arbitrarily heterogeneous subsystems connected in a loop. In the homogeneous case, where all subsystems are identical, the computational complexity reduces to O(1) and an interesting relationship with the infinite case is demonstrated. CSSS matrices can be non-Toeplitz (as compared to circulant matrices), a great expansion of domain, but when restricted to be Toeplitz (and thus circulant), the arithmetic reduces to O(1), a huge cost-savings. The procedures are demonstrated on two computational examples, using a freely available MATLAB toolbox implementation of these algorithms.

关键词： computational methods cyclic interconnection structures large scale systems network analysis and control

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