修正PRP共轭梯度方法求解无约束最优化问题

基于著名的PRP共轭梯度方法,利用CG_DESCENT共轭梯度方法的结构,本文提出了一种求解大规模无约束最优化问题的修正PRP共轭梯度方法。该方法在每一步迭代中均能够产生一个充分下降的搜索方向,且独立于任何线搜索条件。在标准Wolfe线搜索条件下,证明了修正PRP共轭梯度方法的全局收敛性和线性收敛速度。数值结果展示了修正PRP方法对给定的测试问题是非常有效的。     

供应商不确定情景下药品物流多中心选址优化研究

根据国家4+7药品带量集中采购评审标准,基于药品生产企业生产质量、供应能力、相关资质和同类药品参标结果等数据进行梳理和分析,针对药品供应商不确定情景下药品物流多中心选址问题,构建药品物流整体费用最优的多中心选址模型,设计多阶段改进禁忌搜索算法,最后通过4+7带量集中采购具体算例对模型和算法进行验证,结果显示该模型和算法是可行和有效的。     

Lattice models of peptide aggregation: evaluation of conformational search algorithms

We present a series of conformational search calculations on the aggregation of short peptide fragments that form fibrils similar to those seen in many protein mis-folding diseases. The proteins were represented by a face-centered cubic lattice model with the conformational energies calculated using the Miyazawa-Jernigan potential. The searches were performed using algorithms based on the Metropolis Monte Carlo method, including simulated annealing and replica exchange. We also present the results of searches using the tabu search method, an algorithm that has been used for many optimization problems, but has rarely been used in protein conformational searches. The replica exchange algorithm consistently found more stable structures then the other algorithms, and was particularly effective for the octamers and larger systems.     

β微管蛋白中紫杉醇(Taxol)结合腔的性质分析

采用多拷贝同时搜寻法(MCSS), 并结合现有微管抑制剂的SAR及3D-QSAR对β微管蛋白中Taxol(紫杉醇)结合腔的性质进行了分析. 结构研究结果表明, Taxol结合腔以疏水性质为主, 并指出官能团分布的具体位置: 在Phe270上方(Leu361-Pro272-Leu273-Leu228之间)的弧形区域、Asp26羧基下方及其与Glu22羧基之间、M-loop的中部, 以及Asp224内侧且靠近Arg276的胍基的位置. 而Asp224的内侧又是新提出的结合位点. 研究结果符合现有微管抑制剂的SAR, 为现有抗肿瘤药物的结构改造以及小分子微管抑制剂设计提供了理论依据.     

A window fourier domain search system

A search system is presented that utilizes Fourier domain data. This system removes dominating features from the infrared absorbance data, transforms the data into the Fourier domain and performs a complete library search. The actual matching algorithm is very simple and excellent search results were attained using 16 cm^–1 resolution infrared absorbance spectra before transformation. This method can be used to distinguish very similar spectra that cannot be distinguished by many other search methods.     

Conformational analysis of [Met5]-enkephalin: Solvation and ionization considerations

[Met5]-Enkephalin has the sequence Tyr-Gly-Gly-Phe-Met. Only the extended conformation of the peptide has been observed by X-ray crystallography. Nuclear magnetic resonance spectroscopy supports the presence of a turn at Gly 3 and Phe 4 in dimethyl sulfoxide. In this study, the peptide conformational states and thermodynamic properties are understood in terms of ionization state and solvent environment. In the calculation, final conformations obtained from multiple independent Monte Carlo simulated annealing conformational searches are starting points for molecular dynamics simulations. In an aqueous environment given by the use of solvation free energy and the zwitterionic state, dominant structural motifs computed are G-P Type II bend, G-G Type II bend, and G-G Type I bend motifs, in order of increasing free energy. In the calculation of the peptide with neutral N- and C-termini and solvation free energy, the extended conformer dominates (by at least a factor of 2.5), and the conformation of another low free energy conformer superimposes well on the pharmacophoric groups of morphine. Neutralization of charge and solvation induce and stabilize the extended conformation, respectively. A mechanism of inter-conversion between the extended conformer and three bent conformers is supported by /-scatter plots, and by the conformer relative free energies. An estimate of the entropy change of receptor unbinding is 8.3 cal K-1 mol-1, which gives rise to a -2.5 kcal/mol entropy contribution to the free energy of unbinding at 25 °C. The conformational analysis methodology described here should be useful in studies on short peptides and flexible protein surface loops that have important biological implications.     

Observations of trends for singular values and eigenvectors from library searching ultraviolet-visible spectra with spectral subtraction

A promising procedure for computerized library searching and identification of ultraviolet-visible spectra for one- and two-component mixtures is evaluated. The procedure is based on singular value decomposition and utilizes band position and shape. Searching more than one library spectrum at a time is possible. Library spectra which have similar spectra (collinear) with the sample and each other are indicated by two measures. First, a large condition index must be obtained, and second, two or more large variance-decomposition proportions in the same row need to be associated with the large condition index. The searching procedure has a significant degree of differentiation between the actual sample and potential candidates and is compared with the dot product, Euclidean distance and the correlation coefficient.     

A proposal for the molecular basis of μ and δ opiate receptor differentiation based on modeling of two types of cyclic enkephalins and a narcotic alkaloid

Summary The molecular basis underlying the divergent receptor selectivity of two cyclic opioid peptides Tyr-c[N -d-Orn²-Gly-Phe-Leu-] (c-ORN) and [d-Pen², l-Cys⁵]-enkephalinamide (c-PEN) was investigated using a molecular modeling approach. Ring closure and conformational searching procedures were used to determine low-energy cyclic backbone conformers. Following reinsertion of amino acid side chains, the narcotic alkaloid 7-[(1R)-1-methyl-1-hydroxy-3-phenylpropyl]-6,14-endoethenotetrahydro oripavine (PEO) was used as a flexible template for bimolecular superpositions with each of the determined peptide ring conformers using the coplanarity and cocentricity of the phenolic rings as the minimum constraint. A vector space of PEO, accounting for all possible orientations for the C₂₁-aromatic ring of PEO served as a geometrical locus for the aromatic ring of the Phe⁴ residue in the opioid peptides. Although a vast number of polypeptide conformations satisfied the criteria of the opiate pharmacophore, they could be grouped into three classes differing in magnitude and sign of the torsional angle values of the tyrosyl side chain. Only class III conformers for both c-ORN and c-PEN, having tyramine dihedral angles ₁ =–150° ± 30° and ₂=–155° ± 20°, had significant structural and conformational properties that were mutually compatible while respecting the PEO vector space. Comparison of these properties in the context of the divergent receptor selectivity of the studied opioid peptides suggests that the increased distortion of the peptide backbone in the closure region of c-PEN together with the pendant ,-dimethyl group, combine to generate a steric volume which is absent in c-ORN and that may be incompatible with a restrictive topography of the receptor. The nature and stereo-chemistry of substituents adjacent to the closure region of the peptides could also modulate receptor selection by interacting with a charged () or neutral () subsite.     

On the convergence of the LJ search method

The convergence of the Luus-Jaakola search method for unconstrained optimization problems is established.Notation E _n Euclideann-space - f Gradient off(x) - ² f Hessian matrix - (·) ^T Transpose of (·) - I Index set {1, 2, ...,n} - [x _i1 ^*(j) ] Point around which search is made in the (j + 1)th iteration, i.e., [x _1l ^*(j) ,x _2l ^*(j) ,...,x _n1 ^*(j) ] - r _i ⁽ⁱ⁾ Range ofx _il ^*(i) in the (j + 1)th iteration - l ₁ min_i {r _i ⁽⁰⁾ } - l ₂ min_i {r _i ⁽⁰⁾ } - A _j Region of search in thejth iteration, i.e., {x E _n:x _il ^*(j-1) –0.5r _i ^(j-1) x _ix _il ^*(j-1) +0.5r _i ^(j-1) ,i I} - S _j Closed sphere with center origin and radius _j - Reduction factor in each iteration - 1– - (·) Gamma function Many discussions with Dr. S. N. Iyer, Professor of Electrical Engineering, College of Engineering, Trivandrum, India, are gratefully acknowledged. The author has great pleasure to thank Dr. K. Surendran, Professor, Department of Electrical Engineering, P.S.G. College of Technology, Coimbatore, India, for suggesting this work.     

Properties of the random search in global optimization

From theorems which we prove about the behavior of gaps in a set ofN uniformly random points on the interval [0, 1], we determine properties of the random search procedure in one-dimensional global optimization. In particular, we show that the uniform grid search is better than the random search when the optimum is chosen using the deterministic strategy, that a significant proportion of large gaps are contained in the uniformly random search, and that the error in the determination of the point at which the optimum occurs, assuming that it is unique, will on the average be twice as large using the uniformly random search compared with the uniform grid. In addition, some of the properties of the largest gap are verified numerically, and some extensions to higher dimensions are discussed. The latter show that not all of the conclusions derived concerning the inadequacies of the one-dimensional random search extend to higher dimensions, and thaton average the random search is better than the uniform grid for dimensions greater than 6.This paper is based on work started in the Statistics Department of Princeton University when the first author was visiting as a Research Associate. Part of this research was supported by the Office of Naval Research, Contract No. 0014-67-A-0151-0017, and by the US Army Research Office—Durham, Contract No. DA-31-124-ARO-D-215.2 The authors wish to thank B. Omodei for his careful work in preparing the programs for the results of Figs. 1–2 and Table 1. The computations were performed on the IBM 360/50 of the Australian National University's Computer Centre. Thanks are also due to R. Miles for suggestions regarding the extension of the results to multidimensional regions, and to P. A. P. Moran and R. Brent for suggestions regarding the evaluation of the integral ₀ ¹ ... ^0/1 (x ₁ ² + ... +x _n ^/2 )^1/2 dx ₁ ...dx _n.