scholarly journals A homology identification method that combines protein sequence and structure information

1998 ◽  
Vol 7 (12) ◽  
pp. 2499-2510 ◽  
Author(s):  
Lihua Yu ◽  
James V. White ◽  
Temple F. Smith
Keyword(s):  
Protein Sequence ◽  
Structure Information ◽  
Identification Method

scholarly journals Prediction of High-Risk Types of Human Papillomaviruses Using Reduced Amino Acid Modes

2020 ◽  
Vol 2020 ◽  
pp. 1-10
Author(s):  
Xinnan Xu ◽  
Rui Kong ◽  
Xiaoqing Liu ◽  
Pingan He ◽  
Qi Dai
Keyword(s):  
Amino Acids ◽  
Cervical Cancer ◽  
Amino Acid ◽  
High Risk ◽  
Protein Sequence ◽  
Human Papillomaviruses ◽  
Prediction Methods ◽  
Structure Information ◽  
Hpv Types ◽  
High Risk Hpv

A human papillomavirus type plays an important role in the early diagnosis of cervical cancer. Most of the prediction methods use protein sequence and structure information, but the reduced amino acid modes have not been used until now. In this paper, we introduced the modes of reduced amino acids to predict high-risk HPV. We first reduced 20 amino acids into several nonoverlapping groups and calculated their structure and physicochemical modes for high-risk HPV prediction, which was tested and compared with the existing methods on 68 samples of known HPV types. The experiment result indicates that the proposed method achieved better performance with an accuracy of 96.49%, indicating that the reduced amino acid modes might be used to improve the prediction of high-risk HPV types.

Electron crystallographic determination of the 3-D structure of staurolite at atomic resolution

1991 ◽  
Vol 49 ◽  
pp. 540-541
Author(s):  
Kenneth H. Downing ◽  
Hu Meisheng ◽  
Hans-Rudolf Went ◽  
Michael A. O'Keefe
Keyword(s):  
High Resolution ◽  
Three Dimensional ◽  
High Resolution Electron Microscopy ◽  
Atomic Resolution ◽  
Dimensional Structure ◽  
Structure Information ◽  
Resolution Electron ◽  
Scattering Effects ◽  
High Resolution Images ◽  
Effects Of Radiation

With current advances in electron microscope design, high resolution electron microscopy has become routine, and point resolutions of better than 2Å have been obtained in images of many inorganic crystals. Although this resolution is sufficient to resolve interatomic spacings, interpretation generally requires comparison of experimental images with calculations. Since the images are two-dimensional representations of projections of the full three-dimensional structure, information is invariably lost in the overlapping images of atoms at various heights. The technique of electron crystallography, in which information from several views of a crystal is combined, has been developed to obtain three-dimensional information on proteins. The resolution in images of proteins is severely limited by effects of radiation damage. In principle, atomic-resolution, 3D reconstructions should be obtainable from specimens that are resistant to damage. The most serious problem would appear to be in obtaining high-resolution images from areas that are thin enough that dynamical scattering effects can be ignored.

Structure Information From Electron Diffraction Intensities

1990 ◽  
Vol 48 (2) ◽  
pp. 516-517
Author(s):  
J. Gjønnes ◽  
N. Bøe ◽  
K. Gjønnes
Keyword(s):  
Computational Effort ◽  
Unit Cell ◽  
Small Unit ◽  
Structure Information ◽  
Dispersion Surface ◽  
Integrated Intensity ◽  
The One ◽  
Image Position ◽  
Convergent Beam ◽  
Beam Patterns

Structure information of high precision can be extracted from intentsity details in convergent beam patterns like the one reproduced in Fig 1. From low order reflections for small unit cell crystals,bonding charges, ionicities and atomic parameters can be derived, (Zuo, Spence and O’Keefe, 1988; Zuo, Spence and Høier 1989; Gjønnes, Matsuhata and Taftø, 1989) , but extension to larger unit cell ma seem difficult. The disks must then be reduced in order to avoid overlap calculations will become more complex and intensity features often less distinct Several avenues may be then explored: increased computational effort in order to handle the necessary many-parameter dynamical calculations; use of zone axis intensities at symmetry positions within the CBED disks, as in Figure 2 measurement of integrated intensity across K-line segments. In the last case measurable quantities which are well defined also from a theoretical viewpoint can be related to a two-beam like expression for the intensity profile:With as an effective Fourier potential equated to a gap at the dispersion surface, this intensity can be integrated across the line, with kinematical and dynamical limits proportional to and at low and high thickness respctively (Blackman, 1939).

Least-square refinement of structure parameters from CBED integrated intensities: application to determination of temperature factors in Y BA2CU3O7

1992 ◽  
Vol 50 (2) ◽  
pp. 1456-1457
Author(s):  
Kjersti Gjønnes ◽  
Jon Gjønnes
Keyword(s):  
Least Square ◽  
Measured Intensity ◽  
Structure Information ◽  
Accurate Temperature ◽  
Least Square Fit ◽  
Case Application ◽  
Integrated Intensities ◽  
Temperature Factors ◽  
Narrow Bands

Electron diffraction intensities can be obtained at large scattering angles (sinθ/λ ≥ 2.0), and thus structure information can be collected in regions of reciprocal space that are not accessable with other diffraction methods. LACBED intensities in this range can be utilized for determination of accurate temperature factors or for refinement of coordinates. Such high index reflections can usually be treated kinematically or as a pertubed two-beam case. Application to Y Ba2Cu3O7 shows that a least square refinememt based on integrated intensities can determine temperature factors or coordinates.LACBED patterns taken in the (00l) systematic row show an easily recognisable pattern of narrow bands from reflections in the range 15 < l < 40 (figure 1). Integrated intensities obtained from measured intensity profiles after subtraction of inelastic background (figure 2) were used in the least square fit for determination of temperature factors and refinement of z-coordinates for the Ba- and Cu-atoms.

Simulations of high-resolution images of amorphous silicon films

1986 ◽  
Vol 44 ◽  
pp. 544-545
Author(s):  
G. Y. Fan ◽  
J. M. Cowley
Keyword(s):  
Electron Microscope ◽  
High Frequency ◽  
Fourier Transformation ◽  
Amorphous Materials ◽  
Low Frequency ◽  
Chromatic Aberration ◽  
Structure Information ◽  
Frequency Components ◽  
High Resolution Images ◽  
Spatial Frequency Spectrum

It is well known that the structure information on the specimen is not always faithfully transferred through the electron microscope. Firstly, the spatial frequency spectrum is modulated by the transfer function (TF) at the focal plane. Secondly, the spectrum suffers high frequency cut-off by the aperture (or effectively damping terms such as chromatic aberration). While these do not have essential effect on imaging crystal periodicity as long as the low order Bragg spots are inside the aperture, although the contrast may be reversed, they may change the appearance of images of amorphous materials completely. Because the spectrum of amorphous materials is continuous, modulation of it emphasizes some components while weakening others. Especially the cut-off of high frequency components, which contribute to amorphous image just as strongly as low frequency components can have a fundamental effect. This can be illustrated through computer simulation. Imaging of a whitenoise object with an electron microscope without TF limitation gives Fig. 1a, which is obtained by Fourier transformation of a constant amplitude combined with random phases generated by computer.

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