scholarly journals Sequence and Structure Analysis of Biological Molecules Based on Computational Methods

2015 ◽  
Vol 2015 ◽  
pp. 1-3
Author(s):  
Jia-Feng Yu ◽  
Yue-Dong Yang ◽  
Xiao Sun ◽  
Ji-Hua Wang
Keyword(s):  
Structure Analysis ◽  
Computational Methods ◽  
Biological Molecules

scholarly journals The optimal DFT approach in DP4 NMR structure analysis – pushing the limits of relative configuration elucidation

2019 ◽  
Vol 17 (24) ◽  
pp. 5886-5890 ◽  
Author(s):  
Kristaps Ermanis ◽  
Kevin E. B. Parkes ◽  
Tatiana Agback ◽  
Jonathan M. Goodman
Keyword(s):  
Structure Analysis ◽  
Computational Methods ◽  
Structure Elucidation ◽  
Nmr Structure ◽  
Relative Configuration ◽  
Computational Structure

What computational methods should be used to achieve the most reliable result in computational structure elucidation? A study on the effect of quality and quantity of geometries on computational NMR structure elucidation performance is reported.

Computational Methods; Tool for Electronic Structure Analysis of Solids

2005 ◽  
Author(s):  
Rashid Ahmed ◽  
Maqsood Ahmed ◽  
M. A. Saeed ◽  
Fazal‐e‐Aleem
Keyword(s):  
Electronic Structure ◽  
Structure Analysis ◽  
Computational Methods

scholarly journals GIC: A computational method for predicting the essentiality of long noncoding lncRNAs

2017 ◽  
Author(s):  
Pan Zeng ◽  
Ji Chen ◽  
Yuan Zhou ◽  
Jichun Yang ◽  
Qinghua Cui
Keyword(s):  
Computational Methods ◽  
High Performance ◽  
Noncoding Rnas ◽  
Web Server ◽  
Long Noncoding Rnas ◽  
Computational Method ◽  
Biological Molecules ◽  
Sequence Information ◽  
Protein Coding ◽  
Protein Coding Genes

ABSTRACTMeasuring the essentiality of genes is critically important in biology and medicine. Some bioinformatic methods have been developed for this issue but none of them can be applied to long noncoding RNAs (lncRNAs), one big class of biological molecules. Here we developed a computational method, GIC (Gene Importance Calculator), which can predict the essentiality of both protein-coding genes and lncRNAs based on RNA sequence information. For identifying the essentiality of protein-coding genes, GIC is competitive with well-established computational scores. More important, GIC showed a high performance for predicting the essentiality of lncRNAs. In an independent mouse lncRNA dataset, GIC achieved an exciting performance (AUC=0.918). In contrast, the traditional computational methods are not applicable to lncRNAs. As a public web server, GIC is freely available at http://www.cuilab.cn/gic/.

scholarly journals Structural genomics: Computational methods for structure analysis

2003 ◽  
Vol 12 (9) ◽  
pp. 1813-1821 ◽  
Author(s):  
Sharon Goldsmith-Fischman ◽  
Barry Honig
Keyword(s):  
Structure Analysis ◽  
Computational Methods ◽  
Structural Genomics

Elastic Scattering in Electron Microscopy

1973 ◽  
Vol 31 ◽  
pp. 252-253
Author(s):  
J. Langmore ◽  
M. Isaacson ◽  
J. Wall ◽  
A. V. Crewe
Keyword(s):  
Electron Microscopy ◽  
Elastic Scattering ◽  
Cross Section ◽  
Quantum Noise ◽  
Dark Field ◽  
Elastic Cross Section ◽  
Biological Molecules ◽  
Dark Field Microscopy ◽  
Field Systems ◽  
Effects Of Radiation

High resolution dark field microscopy is becoming an important tool for the investigation of unstained and specifically stained biological molecules. Of primary consideration to the microscopist is the interpretation of image Intensities and the effects of radiation damage to the specimen. Ignoring inelastic scattering, the image intensity is directly related to the collected elastic scattering cross section, σɳ, which is the product of the total elastic cross section, σ and the eficiency of the microscope system at imaging these electrons, η. The number of potentially bond damaging events resulting from the beam exposure required to reduce the effect of quantum noise in the image to a given level is proportional to 1/η. We wish to compare η in three dark field systems.

3-D reconstruction of molecular shape from microcrystal thin sections

1983 ◽  
Vol 41 ◽  
pp. 748-749
Author(s):  
S. Cusack ◽  
J.-C. Jésior
Keyword(s):  
Three Dimensional ◽  
Molecular Shape ◽  
Biological Molecules ◽  
Fourier Space ◽  
Single Particles ◽  
Thin Sections ◽  
Standard Methods ◽  
X Ray ◽  
X Ray Crystallography ◽  
Dimensional Reconstruction

Three-dimensional reconstruction techniques using electron microscopy have been principally developed for application to 2-D arrays (i.e. monolayers) of biological molecules and symmetrical single particles (e.g. helical viruses). However many biological molecules that crystallise form multilayered microcrystals which are unsuitable for study by either the standard methods of 3-D reconstruction or, because of their size, by X-ray crystallography. The grid sectioning technique enables a number of different projections of such microcrystals to be obtained in well defined directions (e.g. parallel to crystal axes) and poses the problem of how best these projections can be used to reconstruct the packing and shape of the molecules forming the microcrystal.Given sufficient projections there may be enough information to do a crystallographic reconstruction in Fourier space. We however have considered the situation where only a limited number of projections are available, as for example in the case of catalase platelets where three orthogonal and two diagonal projections have been obtained (Fig. 1).

Direct visualization of phase-separated domains in lipid membranes

1978 ◽  
Vol 36 (2) ◽  
pp. 290-291
Author(s):  
S. W. Hui ◽  
T. P. Stewart
Keyword(s):  
Lipid Membranes ◽  
Structural Information ◽  
Freeze Fracture ◽  
Biological Molecules ◽  
Vacuum Drying ◽  
Direct Visualization ◽  
X Ray Diffraction ◽  
Electron Microscopic ◽  
X Ray ◽  
Hydrocarbon Chains

Direct electron microscopic study of biological molecules has been hampered by such factors as radiation damage, lack of contrast and vacuum drying. In certain cases, however, the difficulties may be overcome by using redundent structural information from repeating units and by various specimen preservation methods. With bilayers of phospholipids in which both the solid and fluid phases co-exist, the ordering of the hydrocarbon chains may be utilized to form diffraction contrast images. Domains of different molecular packings may be recgnizable by placing properly chosen filters in the diffraction plane. These domains would correspond to those observed by freeze fracture, if certain distinctive undulating patterns are associated with certain molecular packing, as suggested by X-ray diffraction studies. By using an environmental stage, we were able to directly observe these domains in bilayers of mixed phospholipids at various temperatures at which their phases change from misible to inmissible states.

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