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Mapping a neutralizing epitope on the SARS coronavirus spike protein: computational prediction based on affinity-selected peptides

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JOURNAL OF MOLECULAR BIOLOGY 2006年第1期359卷 190-201页

作者： Tarnovitski, Natalia Matthews, Leslie J. Sui, Jianhua Gershoni, Jonathan M. Marasco, Wayne A. Tel Aviv Univ George S Wise Fac Life Sci Dept Cell Res & Immunol IL-69978 Tel Aviv Israel Harvard Univ Sch Med Dana Farber Canc Inst Dept Canc Immunol & AIDS Boston MA 02115 USA Harvard Univ Sch Med Dept Med Boston MA 02115 USA

Rapid elucidation of neutralizing antibody epitopes on emerging viral pathogens like severe acute respiratory syndrome (SARS) coronavirus (CoV) or highly pathogenic avian influenza H5N1 virus is of great importance for rational design of vaccines against these viruses. Here we combined screening of phage display random peptide libraries with a unique computer algorithm "Mapitope" to identify the discontinuous epitope of 80R, a potent neutralizing human anti-SARS monoclonal antibody against the spike protein. Using two different types of random peptide libraries which display cysteine-constrained loops or linear 13-15-mer peptides, independent panels containing 42 and 18 peptides were isolated, respectively. These peptides, which had no apparent homologous motif within or between the peptide pools and spike protein, were deconvoluted into amino acid pairs (AAPs) by Mapitope and the statistically significant pairs (SSPs) were defined. Mapitope analysis of the peptides was first performed on a theoretical model of the spike and later on the genuine crystal structure. Three clusters (A, B and C) were predicted on both structures with remarkable overlap. Cluster A ranked the highest in the algorithm in both models and coincided well with the sites of spike protein that are in contact with the receptor, consistent with the observation that 80R functions as a potent entry inhibitor. This study demonstrates that by using this novel strategy one can rapidly predict and identify a neutralizing antibody epitope, even in the absence of the crystal structure of its target protein. (c) 2006 Elsevier Ltd. All rights reserved.

关键词： SARS antibody epitope Mapitope computational algorithm

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COMPUTER-BASED TECHNIQUES FOR SOLVING PROBLEMS OF APPLIED AND computational MATHEMATICS WITH GIVEN QUALITY CHARACTERISTICS

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CYBERNETICS AND SYSTEMS ANALYSIS 2006年第5期42卷 641-648页

作者： Sergienko, I. V. Zadiraka, V. K. Babich, M. D. Berezovskii, A. I. Besarab, P. N. Lyudvichenko, V. A. Natl Acad Sci Ukraine VM Glushkov Inst Cybernet Kiev Ukraine 2Ukrainian Acad Foreign Trade Kiev Ukraine Int Acad Human Resource Management MAUP Kiev Ukraine

The paper is concerned with computer-based techniques for the choice and development of computational resources and their efficient use to find an approximate solution with a given accuracy in a limited processor time.

关键词： computer-based techniques mathematical model of applied problem computational model computational process computational algorithm estimates of quality characteristics of computational algorithm

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Stochastic models (cooperative and non-cooperative) for NMR analysis of the hetero-association of aromatic molecules in aqueous solution

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CHEMICAL PHYSICS 2006年第1-2期321卷 25-33页

作者： Evstigneev, MP Davies, DB Veselkov, AN Sevastopol Natl Tech Univ Dept Phys UA-99053 Sevastopol Crimea Ukraine Univ London Birkbeck Coll Sch Biol & Chem Sci London WC1E 7HX England

Stochastic cooperative (STOCH-C) and non-cooperative (STOCH-NC) models have been developed for NMR analysis of the hetero-association of aromatic compounds in solution, in order to take into account all physically meaningful association reactions of molecules in which there are no limitations on the lengths of the aggregates and complexes. These algorithmical approaches are compared with previously published basic (BASE) and generalized (GEN) analytical statistical thermodynamical models of hetero-association of biologically active aromatic molecules using the same sets of published NMR data measured under the same solution conditions (0.1 M phosphate buffer, pD = 7.1, T = 298 K). It is shown that, within experimental errors, the BASE analytical model may be used to describe molecular systems characterized by relatively small contributions of hetero-association reactions, whereas the GEN model may be applied to hetero-association reactions of any aromatic compound with different self-association properties. The STOCH-C computational algorithm enabled the effect on hetero-association of the interactions of molecules with different cooperativity parameters of self-association to be estimated for the first time and it is proposed that the algorithm for the stochastic models has great potential for detailed investigation and understanding of the interactions of aromatic molecules in solution. (c) 2005 Elsevier B.V. All rights reserved.

关键词： hetero-association model computational algorithm NMR chemical shifts cooperativity parameter aromatic molecules

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computational algorithms for multiscale identification of nonlinearities in Hammerstein systems with random inputs

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IEEE TRANSACTIONS ON SIGNAL PROCESSING 2005年第1期53卷 360-364页

作者： Sliwinski, P Hasiewicz, Z Wroclaw Univ Technol Inst Engn Cybernet PL-50370 Wroclaw Poland

There are well-known procedures for computing values of compactly supported wavelets in binary grid points. Such algorithms are inherently well suited for solving system identification tasks with fixed input design. We show that they can be also efficiently used for the solution of system identification problems with random x-variables.

关键词： Compactly supported wavelets computational algorithm Hammerstein system system identification.

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Finding the response matrix to the external action from a subspace for a discrete linear stochastic dynamical system

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computational Mathematics and Mathematical Physics 2006年第7期46卷 1155-1167页

作者： Martynov, R.S. Nechepurenko, Yu.M. Institute of Numerical Mathematics Russian Academy of Sciences Moscow 119991 ul. Gubkina 8 Russian Federation

For a discrete linear stochastic dynamical system, computation of the response matrix to the external action from a subspace using given observational data is examined. An algorithm is proposed and substantiated that makes it possible to improve the numerical accuracy and to reduce the amount of observational data compared to the general case where an arbitrary external action is allowed. As an illustration, a discrete system arising in the analysis of a linear stochastic dynamical continuous-time system is considered more thoroughly. Some numerical results are presented. © MAIK "Nauka/Interperiodica" (Russia), 2006.

关键词： computational algorithm Discrete stochastic dynamical system External action from a subspace Response matrix

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Social sharing and risk reduction - Exploring a computational algorithm for the psychology of windfall gains

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EVOLUTION AND HUMAN BEHAVIOR 2002年第1期23卷 11-33页

作者： Kameda, T Takezawa, M Tindale, RS Smith, CM Hokkaido Univ Dept Behav Sci Kita Ku Sapporo Hokkaido 0600810 Japan Max Planck Inst Human Dev D-14195 Berlin Germany Loyola Univ Dept Psychol Chicago IL 60626 USA Grand Valley State Univ Dept Psychol Allendale MI 49401 USA

Sharing important resources widely beyond direct kin group members is one of the core features characterizing human societies. Moreover, generalized exchange involving many community members (e.g., meat sharing in bands) seems to be a uniquely human practice. This paper explores a computational algorithm for the psychology of social sharing that may underlie such practices, based on the risk-reduction hypothesis in food sharing of Kaplan and Hill [Curr. Anthropol. 26 (1985) 223]. We predicted that, independent of the amount of effort actually invested, uncertainty involved in resource acquisition is a key factor that triggers the psychology of social sharing for both acquirers and nonacquirers of a resource. It was also predicted that the "windfall effect" is independent of individual preferences as to modem distributive ideologies. Four multisample/multimethod studies, using Japanese and American participants, and laboratory as well as vignette experiments, supported these predictions: although the identical fungible resource (money) was under consideration, different psychological processes were triggered, depending on the degree of uncertainty involved in the money acquisition. Implications of the windfall effect for egalitarianism in resource sharing, observed not only in hunter-gatherer bands but also in highly industrialized societies, are discussed. (C) 2002 Elsevier Science Inc. All rights reserved.

关键词： resource sharing risk reduction computational algorithm egalitarianism

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Control parametrization enhancing transform to optimal control problems

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NONLINEAR ANALYSIS-THEORY METHODS & APPLICATIONS 2005年第5-7期63卷 E2223-E2236页

作者： Teo, K. L. Curtin Univ Technol Dept Math & Stat Perth WA Australia

In this paper, we consider a class of constrained optimal control problems subject to canonical constraints. The control parametrization enhancing transform can be used together with the control parametrization technique to develop an efficient computational method for solving this class of optimal control problem. The purpose of this paper is to present this computational method as well as the supporting convergence analysis in a mathematically rigorous manner. (C) 2005 Elsevier Ltd. All rights reserved.

关键词： Optimal control computation Control parameterization enhancing transform computational algorithm

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A convexity preserving scheme for conservative advection transport

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JOURNAL OF computational PHYSICS 2004年第2期198卷 389-402页

作者： Xiao, F Peng, XD Tokyo Inst Technol Dept Energy Sci Midori Ku Yokohama Kanagawa 2268502 Japan JAMSTEC Earth Simulator Ctr Kanazawa Ku Yokohama Kanagawa 2360001 Japan

A simple and practical scheme for advection transport equation is presented. The scheme, namely piecewise rational method (PRM), is a variant of the existing piecewise parabolic method (PPM) of Colella and Woodward (1984). Instead of the parabolic function, a rational function is used for the reconstruction. Making use of the convexity preserving nature of the rational function enables us to obtain oscillation-less numerical solutions, but avoids the adjustments of the cell-interface values to enforce the monotonicity in PPM. The PRM is very simple and computationally efficient. Our numerical results show that PRM is competitive to the PPM in many aspects, such as numerical accuracy and shape-preserving property. (C) 2004 Elsevier Inc. All rights reserved.

关键词： advection transport computational algorithm rational interpolation convexity preserving numerical oscillation mass conservation

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A general alternative procedure for solving negative degree of difficulty problems in geometric programming

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computational OPTIMIZATION AND APPLICATIONS 2004年第1期27卷 83-93页

作者： Alejandre, JL Allueva, A Gonzalez, JM Univ Zaragoza Dept Appl Math E-50009 Zaragoza Spain

The degree of difficulty is an important concept in classical geometric programming theory. The dual problem is often infeasible when the degree of difficulty is negative and little has been published on this topic. In this paper, an alternative procedure is developed to find the optimal solution for the posynomial geometric programming problem with a negative degree of difficulty. First an equivalent problem was constructed with a positive degree of difficulty and the general posynomial geometric programming problem was solved using an original method previously developed by the authors. This method avoids the difficulty of nondifferentiability of the dual objective function in the classical methods classified as dual. It also avoids the problem that appears when the feasible region for the dual problem is formed by an inconsistent system of linear equations.

关键词： geometric programming nonlinear optimization degree of difficulty computational algorithm

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A time integration algorithm based on the state transition matrix for structures with time varying and nonlinear properties

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COMPUTERS & STRUCTURES 2003年第6期81卷 349-357页

作者： Bartels, RE NASA Langley Res Ctr Aeroelast Branch Hampton VA 23681 USA

A variable order method of integrating the structural dynamics equations that is based on the state transition matrix has been developed. The method has been evaluated for linear time variant and nonlinear systems of equations. When the time variation of the system can be modeled exactly by a polynomial it produces nearly exact solutions for a wide range of time step sizes. Solutions of a model nonlinear dynamic response exhibiting chaotic behavior have been computed. Accuracy of the method has been demonstrated by comparison with solutions obtained by established methods. Published by Elsevier Science Ltd.

关键词： computational algorithm linear time variant nonlinear state transition matrix structural dynamics chaos

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