Protein-ligand binding free energy estimation using molecular mechanics and continuum electrostatics. Application to HIV-1 protease inhibitors

A method is proposed for the estimation of absolute binding free energy of interaction between proteins and ligands. Conformational sampling of the protein-ligand complex is performed by molecular dynamics (MD) in vacuo and the solvent effect is calculated a posteriori by solving the Poisson or the Poisson-Boltzmann equation for selected frames of the trajectory. The binding free energy is written as a linear combination of the buried surface upon complexation, SASbur, the electrostatic interaction energy between the ligand and the protein, Eelec, and the difference of the solvation free energies of the complex and the isolated ligand and protein, deltaGsolv. The method uses the buried surface upon complexation to account for the non-polar contribution to the binding free energy because it is less sensitive to the details of the structure than the van der Waals interaction energy. The parameters of the method are developed for a training set of 16 HIV-1 protease-inhibitor complexes of known 3D structure. A correlation coefficient of 0.91 was obtained with an unsigned mean error of 0.8 kcal/mol. When applied to a set of 25 HIV-1 protease-inhibitor complexes of unknown 3D structures, the method provides a satisfactory correlation between the calculated binding free energy and the experimental pIC5o without reparametrization.     

Interval estimation of the critical value in a general linear model

Summary This paper concerns interval estimation of the critical value θ which satisfies under the general linear model,Y _i =μ(x _i )+ε _i (i=1,2,···), where for and the functional forms off _j ^′ s are known. From an asymptotic expansion it is shown that, under reasonable conditions, the limiting distribution of is normal. Thus in the large-sample case a confidence interval for θ can be obtained. Such a result is useful when one is interested in carrying out a retrospective analysis rather than designing the experiment (as in the Kiefer-Wolfowitz procedure). In Section 3 a sequential procedure is considered for confidence intervals with fixed width 2d. It is shown that, for a given stopping variableN, is also asymptotically normal asd→0. Thus the coverage probability converges to 1−α (preassigned) asd→0. An example of application in estimating the phase parameter in circadian rhythms is given for the purpose of illustration. Research partially supported by the NSF Grant DMS-8502346.     

Polyparametric modification equation for estimating thermodynamic properties of energetic nitro compounds

Calculation methods, based on hybrid density-functional theory with the basis sets of B3LYP/ 6-311+G (2d, p)//B3LYP/6-31G(d, p)and B3LYP/6-31+G(d)//B3LYP/6-31G(d, p), were applied to determine the thermodynamic characteristics of various energetic nitro compounds. A parametric modification equation and the least-squares approach were used to identify 21 of the energetic research compounds. The atomization energies of these 21 compounds have an average relative error of 0.21–0.25% of the experimental values. The enthalpy (H _f) and the Gibbs energy (G _f) of formation have mean absolute errors of 10.8–11.4 kJ/ mol (2.6–2.7 kcal/mol) and 10.0–10.3 kJ/mol (2.4 kcal/ mol), respectively. The enthalpy and the Gibbs energy of formation obtained exceed those in the literature obtained by semiempirical calculations. The calibrated least-squares parameters and parametric equations were used to predict H _f and G _f for the five newly developed energetic nitro compounds for further applications.Acknowledgements. The authors would like to thank the National Science Council of the Republic of China for financial support of this work under grant no. NSC-91-2113-M-014-003. The National Center for High-Performance Computing providing the computation facility is also acknowledged.     

病态分析体系有偏估计的研究

运用广义岭估计和Ｌｉｕｋｅｊｉａｎ提出的有偏估计，对病态分析体系进行了数值模拟和实际光度测定，结果表明，广义岭估计显优于最小二乘估计，Ｌｉｕｋｅｊｉａｎ法有功效，可和为解析病态分析体系的化学计量学方法。     

Parameter identification of thermophilic anaerobic degradation of valerate

The considered mathematical model of the decomposition of valerate presents three unknown kinetic parameters, two unknown stoichiometric coefficients, and three unknown initial concentrations for biomass. Applying a structural identifiability study, we concluded that it is necessary to perform simultaneous batch experiments with differenitial conditions for estimating these parameters. Four simultaneous batch experiments were conducted at 55°C, characterized by four different initial acetate concentrations. Product inhibition of valerate degradation by acetate was considered. Practical identification was done optimizing the sum of the multiple determination coefficients for all measured state viariables and for all experiments simultaneously. The estimated values of kinetic parameters and stoichiometric coefficients were characterized by the parameter correlation matrix, the confidence interval, and the student's t-test at 9% significance level with positive results except for the saturation constant, for which more eperiments for improving its identifiability should be conducted. In this article, we discussekinetic parameter estimation methods.     

曲率流的参数化有限元逼近

许多物理现象可以在数学上描述为受曲率驱动的自由界面运动,例如薄膜和泡沫的演变、晶体生长,等等.这些薄膜和界面的运动常依赖于其表面曲率,从而可以用相应的曲率流来描述,其相关自由界面问题的数值计算和误差分析一直是计算数学领域中的难点.参数化有限元法是曲率流的一类有效计算方法,已经能够成功模拟一些曲面在几类基本的曲率流下的演化过程.本文重点讨论曲率流的参数化有限元逼近,它的产生、发展和当前的一些挑战.     

高维稳健主成分聚类方法及其应用研究

随着信息技术的高速发展,每条数据所包含的信息越来越丰富,使得数据不可避免地含有异常值,且随着维数的增加,异常值出现的可能性更大。传统的主成分聚类分析对异常值特別敏感,基于MCD估计的主成分聚类方法虽然对异常值具有防御作用,但是在高维数据下MCD估计的偏差过大,其稳健性显著降低,而且当维数大于观测值个数时MCD估计失效。为此本文提出了基于MRCD估计的稳健主成分聚类方法,数值模拟和实证分析表明,基于MRCD估计的主成分聚类分析的效果优于传统的主成分聚类分析和基于MCD估计的主成分聚类分析,尤其是在维数大于样本观测值的情况下,MRCD估计更为有效。     

Weighted local polynomial estimations of a non-parametric function with censoring indicators missing at random and their applications

In this paper, we consider the weighted local polynomial calibration estimation and imputation estimation of a non-parametric function when the data are right censored and the censoring indicators are missing at random, and establish the asymptotic normality of these estimators. As their applications, we derive the weighted local linear calibration estimators and imputation estimations of the conditional distribution function, the conditional density function and the conditional quantile function, and investigate the asymptotic normality of these estimators. Finally, the simulation studies are conducted to illustrate the finite sample performance of the estimators.     

LOWLAD: a locally weightedL 1 smoothing spline algorithm with cross validated choice of smoothing parameters

The computation ofL ₁ smoothing splines on large data sets is often desirable, but computationally infeasible. A locally weighted, LAD smoothing spline based smoother is suggested, and preliminary results will be discussed. Specifically, one can seek smoothing splines in the spacesW _m (D), with [0, 1] ⁿ D. We assume data of the formy _i =f(t _i )+ _i ,i=1,..., N with {t _i } _i=1 ^N D, the _i are errors withE( _i )=0, andf is assumed to be inW _m . An LAD smoothing spline is the solution,s , of the following optimization problem

Perturbation analysis of theGI/GI/1 queue

We examine a family ofGI/GI/1 queueing processes generated by a parametric family of service time distributions,F(x,), and we show that under suitable conditions the corresponding customer stationary expectation of the system time is twice continuously differentiable with respect to. Expressions for the derivatives are given which are suitable for single run derivative estimation. These results are extended to parameters of the interarrival time distribution and expressions for the corresponding second derivatives (as well as partial second derivatives involving both interarrivai and service time parameters) are also obtained. Finally, we present perturbation analysis algorithms based on these expressions along with simulation results demonstrating their performance.