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31.
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. 相似文献
32.
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. 相似文献
33.
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. 相似文献
34.
Villanueva J Villegas V Querol E Avilés FX Serrano L 《Journal of mass spectrometry : JMS》2002,37(9):974-984
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. 相似文献
35.
Gelebe AC Kaye PT Klein R Sewry JD Soper AG 《Magnetic resonance in chemistry : MRC》2005,43(11):952-955
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. 相似文献
36.
37.
Least squares estimations have been used extensively in many applications, e.g. system identification and signal prediction. When the stochastic process is stationary, the least squares estimators can be found by solving a Toeplitz or near-Toeplitz matrix system depending on the knowledge of the data statistics. In this paper, we employ the preconditioned conjugate gradient method with circulant preconditioners to solve such systems. Our proposed circulant preconditioners are derived from the spectral property of the given stationary process. In the case where the spectral density functions() of the process is known, we prove that ifs() is a positive continuous function, then the spectrum of the preconditioned system will be clustered around 1 and the method converges superlinearly. However, if the statistics of the process is unknown, then we prove that with probability 1, the spectrum of the preconditioned system is still clustered around 1 provided that large data samples are taken. For finite impulse response (FIR) system identification problems, our numerical results show that annth order least squares estimator can usually be obtained inO(n logn) operations whenO(n) data samples are used. Finally, we remark that our algorithm can be modified to suit the applications of recursive least squares computations with the proper use of sliding window method arising in signal processing applications.Research supported in part by HKRGC grant no. 221600070, ONR contract no. N00014-90-J-1695 and DOE grant no. DE-FG03-87ER25037. 相似文献
38.
Since Dantzig—Wolfe's pioneering contribution, the decomposition approach using a pricing mechanism has been developed for a wide class of mathematical programs. For convex programs a linear space of Lagrangean multipliers is enough to define price functions. For general mathematical programs the price functions could be defined by using a subclass of nondecreasing functions. However the space of nondecreasing functions is no longer finite dimensional. In this paper we consider a specific nonconvex optimization problem min {f(x):h
j
(x)g(x),j=1, ,m, xX}, wheref(·),h
j
(·) andg(·) are finite convex functions andX is a closed convex set. We generalize optimal price functions for this problem in such a way that the parameters of generalized price functions are defined in a finite dimensional space. Combining convex duality and a nonconvex duality we can develop a decomposition method to find a globally optimal solution.This paper is dedicated to Phil Wolfe on the occasion of his 65th birthday. 相似文献
39.
The COSMO-RS method, originally developed for the prediction of liquid-liquid and liquid-vapor equilibrium constants based on quantum chemical calculations, has been extended to solid compounds by addition of a heuristic expression for the Gibbs free energy of fusion. By this addition, COSMO-RS is now capable of a priori prediction of aqueous solubilities of a wide range of typical neutral drug and pesticide compounds. Only three parameters in the heuristic expression have been fitted on a data set of 150 drug-like compounds. On these data an rms deviation of 0.66 log-units was achieved. Later, the model was tested on a set of 107 pesticides, which have been critically selected based on two experimental data sources and by a crosscheck with an independent HQSAR model. On this data set an rms of 0.61 log-units was achieved, without any adjustments to the structurally extremely diverse pesticides. This result verifies the ability of this extended COSMO-RS to predict aqueous solubilities of drugs and pesticides of almost arbitrary structural classes. The new method is COSMO-RSol. 相似文献
40.
Summary A computer interactive identification system is proposed which is based on the relationship between retention and molecular
properties such as the size and shape of polycyclic aromatic hydrocarbons (PAHs). This system offers an automatic analytical
process for liquid chromatography, providing a reliable identification of the separated components. The identification can
be further enhanced by the use of multiple detectors such as a multichannel UV detector. The system can be used for optimization
procedures, resulting in a highly automatic complex analytical system. 相似文献