predForm-Site: Formylation site prediction by incorporating multiple features and resolving data imbalance

Formylation is one of the newly discovered post-translational modifications in lysine residue which is responsible for different kinds of diseases. In this work, a novel predictor, named predForm-Site, has been developed to predict formylation sites with higher accuracy. We have integrated multiple sequence features for developing a more informative representation of formylation sites. Moreover, decision function of the underlying classifier have been optimized on skewed formylation dataset during prediction model training for prediction quality improvement. On the dataset used by LFPred and Formator predictor, predForm-Site achieved 99.5% sensitivity, 99.8% specificity and 99.8% overall accuracy with AUC of 0.999 in the jackknife test. In the independent test, it has also achieved more than 97% sensitivity and 99% specificity. Similarly, in benchmarking with recent method CKSAAP_FormSite, the proposed predictor significantly outperformed in all the measures, particularly sensitivity by around 20%, specificity by nearly 30% and overall accuracy by more than 22%. These experimental results show that the proposed predForm-Site can be used as a complementary tool for the fast exploration of formylation sites. For convenience of the scientific community, predForm-Site has been deployed as an online tool, accessible at http://103.99.176.239:8080/predForm-Site.     

Protein fold recognition

Summary An important, yet seemingly unattainable, goal in structural molecular biology is to be able to predict the native three-dimensional structure of a protein entirely from its amino acid sequence. Prediction methods based on rigorous energy calculations have not yet been successful, and best results have been obtained from homology modelling and statistical secondary structure prediction. Homology modelling is limited to cases where significant sequence similarity is shared between a protein of known structure and the unknown. Secondary structure prediction methods are not only unreliable, but also do not offer any obvious route to the full tertiary structure. Recently, methods have been developed whereby entire protein folds are recognized from sequence, even where little or no sequence similarity is shared between the proteins under consideration. In this paper we review the current methods, including our own, and in particular offer a historical background to their development. In addition, we also discuss the future of these methods and outline the developments under investigation in our laboratory.     

A new method for predicting conduction anesthesia

A new method for predicting conduction anesthesia has been suggested. The method is based on calculation of theP matrix probabilities of interatomic contacts for each molecule of the compounds considered. TheP matrix enables one to evaluate the main tendencies of atoms and atomic groups to interact in biochemical sorption on the nerve fiber surface. The minimum effective concentrations calculated for 25 compounds are in good agreement with the experimental data. The correlation coefficient between the experimental and calculated values is 0.98 when the standard deviation is 0.1 mmol L⁻¹. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 10, pp. 1781–1784, October, 1997.     

Products active on mosquitoes,IV: Synthesis and biological activity of 8-propargyloxy-3,7-dimethyl-2,6-octadienyl/6-octenyl ethers

Summary A series of 8-proparglyoxy-3,7-dimethyl-2,6-octadienyl and 8-propargyloxy-3,7-dimethyl-6-octenyl ethers were prepared from 8-hydroxygeranyl and 8-hydroxycitronellyl ethers, respectively. Almost all compounds showed high toxicity toCulex quinquefaciatus larvae at 1 mgl^–1 dose level.

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Gegen Mücken aktive Produkte, 4. Mitt.: Synthese und biologische Aktivität von 8-Propargyloxy-3,7-dimethyl-2,6-octadienyl/6-octenyl-ethern

Zusammenfassung Eine Reihe von 8-Propargyloxy-3,7-dimethyl-2,6-octadienyl- und 8-propargyloxy-3,7-dimethyl-6-octenyl-ethern wurden aus 8-Hydroxygeranyl- bzw. 8-Hydroxycitronellyl-ethern hergestellt. Fast alle Verbindungen zeigten hoch Toxizität gegenüber Larven vonCulex quinquefaciatus in einer Dosierung von 1 mgl^–1.

     

Incorporation of FT-IR spectral data in a computer-assisted prediction of globular protein structure

Currently, much effort is being directed to the determination of the three-dimensional structure of proteins. Two classes of research are of interest; spectrometric techniques which include Fourier transform infrared (FT-IR) spectrometry, and non-spectrometric prediction schemes. The spectra obtained using FT-IR spectrometry, are analyzed to determine the percentages of alpha-helices, beta-pleated sheets, and non-structured coils in a protein. Unfortunately, FT-IR, as well as other spectrometric techniques, cannot be used to determine the exact secondary structure of a protein reliably. Non-spectrometric prediction methods yield information on the exact secondary structure, but are not always accurate. Most prediction methods relate the primary amino acid sequence to the secondary structure of a protein, allowing sequential secondary structure information for the protein examined to be obtained. The goal of this research is to incorporate FT-IR with a prediction method, resulting in an improvement in the accuracy of the prediction.     

Protein secondary structure and stability determined by combining exoproteolysis and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

In the post-genomic era, several projects focused on the massive experimental resolution of the three-dimensional structures of all the proteins of different organisms have been initiated. Simultaneously, significant progress has been made in the ab initio prediction of protein three-dimensional structure. One of the keys to the success of such a prediction is the use of local information (i.e. secondary structure). Here we describe a new limited proteolysis methodology, based on the use of unspecific exoproteases coupled with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), to map quickly secondary structure elements of a protein from both ends, the N- and C-termini. We show that the proteolytic patterns (mass spectra series) obtained can be interpreted in the light of the conformation and local stability of the analyzed proteins, a direct correlation being observed between the predicted and the experimentally derived protein secondary structure. Further, this methodology can be easily applied to check rapidly the folding state of a protein and characterize mutational effects on protein conformation and stability. Moreover, given global stability information, this methodology allows one to locate the protein regions of increased or decreased conformational stability. All of this can be done with a small fraction of the amount of protein required by most of the other methods for conformational analysis. Thus limited exoproteolysis, together with MALDI-TOF MS, can be a useful tool to achieve quickly the elucidation of protein structure and stability.     

微量元素锡与健康

随着经济的发展，锡及其化合物越来越多地用于现代生活。综述了锡对人体健康的影响，包括：锡的性质、存在，环境污染、抗癌作用以及毒性等方面。     

Benzodiazepine analogues. Part 21. 13C NMR analysis of benzoxathiepine derivatives

The influence of substituents and structure on the 13C NMR spectra of four series of benzoxathiepine derivatives has been investigated. Signal assignments in the 13C NMR spectra have been facilitated by the use of several predictive methods, permitting comparison of their relative efficacy.     

基于储量结构变化的油田开发指标预测与优化数学模型研究

大型油田开发过程中,随着不同类型新储量的不断投入,地质储量结构发生变化,表征油田整体开发技术与经济效果的关键性指标,如产量、可采储量、采收率、储采比、开发成本与操作成本等等也随之改变,其变化规律可用一套数学模型来描述。在开发指标预测基础上,运用多属性决策方法如TOPSIS,可以实现新投产区块组合方案的优选。应用实例表明,本文方法实用、操作性强,可以为油区开发决策提供重要方法与手段。     

灰色GM(1,1,k,k2)模型背景值及时间响应函数优化

本文提出了一种新的带有时间幂次项的灰色GM(1,1,k,k²)模型,给出了其灰微分方程和白化微分方程基本形式。基于最小二乘法获得了该模型参数估计值,并推导了该模型时间响应函数。鉴于GM(1,1,k,k²)模型灰微分方程与白化微分方程之间存在跳跃关系,首先对灰微分方程的背景值进行了优化,并推导了优化后的背景值计算公式。为了克服初始值的影响,根据误差平方和最小,进一步优化了GM(1,1,k,k²)模型时间响应函数。最后,该优化后的GM(1,1,k,k²)模型被应用于软土地基沉降预测,获得了较好的模拟预测效果,说明模型是可行的。