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.     

Computer modelling of the conformational equilibrium of 2-and 2,5,5-substituted 1,3,2-dioxaborinanes

Empirical, semiempirical, and nonempirical quantum-chemical methods were used to study the conformational equilibrium of 2,5,5-substituted 1,3,2-dioxaborinanes. The sofa invertomers were found to correspond to the local and global minima on the potential energy surface. The position of the equilibrium between these forms is a function of the substituents at C₍₅₎ of the heterocycle. __________ Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 12, pp. 1860–1865, December, 2007.     

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.     

Applications of maximum likelihood principal component analysis: incomplete data sets and calibration transfer

The application of a new method to the multivariate analysis of incomplete data sets is described. The new method, called maximum likelihood principal component analysis (MLPCA), is analogous to conventional principal component analysis (PCA), but incorporates measurement error variance information in the decomposition of multivariate data. Missing measurements can be handled in a reliable and simple manner by assigning large measurement uncertainties to them. The problem of missing data is pervasive in chemistry, and MLPCA is applied to three sets of experimental data to illustrate its utility. For exploratory data analysis, a data set from the analysis of archeological artifacts is used to show that the principal components extracted by MLPCA retain much of the original information even when a significant number of measurements are missing. Maximum likelihood projections of censored data can often preserve original clusters among the samples and can, through the propagation of error, indicate which samples are likely to be projected erroneously. To demonstrate its utility in modeling applications, MLPCA is also applied in the development of a model for chromatographic retention based on a data set which is only 80% complete. MLPCA can predict missing values and assign error estimates to these points. Finally, the problem of calibration transfer between instruments can be regarded as a missing data problem in which entire spectra are missing on the ‘slave’ instrument. Using NIR spectra obtained from two instruments, it is shown that spectra on the slave instrument can be predicted from a small subset of calibration transfer samples even if a different wavelength range is employed. Concentration prediction errors obtained by this approach were comparable to cross-validation errors obtained for the slave instrument when all spectra were available.     

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.     

排序集抽样下Inverse Rayleigh分布的Fisher信息量及其在参数估计中的应用

文章分别在简单随机抽样和排序集抽样下研究了Inverse Rayleigh分布中对应样本所含刻度参数θ的Fisher信息量.数值结果表示,同等样本容量的排序集样本比简单随机样本提供更多关于θ的信息.接着分别基于简单随机样本和排序集样本构造了θ的一些优良估计,并对估计结果进行了数值比较.     

Data loci in algebraic optimization

We consider parametric optimization problems from an algebraic viewpoint. The idea is to find all of the critical points of an objective function thereby determining a global optimum. For generic parameters (data) in the objective function the number of critical points remains constant. This number is known as the algebraic degree of an optimization problem. In this article, we go further by considering the inverse problem of finding parameters of the objective function so it gives rise to critical points exhibiting a special structure. For example if the critical point is in the singular locus, has some symmetry, or satisfies some other algebraic property. Our main result is a theorem describing such parameters.     

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.