AMINONET– a tool to construct and visualize amino acid networks, and to calculate topological parameters

2010 ◽  
Vol 43 (2) ◽  
pp. 367-369 ◽  
Author(s):  
Md. Aftabuddin ◽  
Sudip Kundu
Keyword(s):  
Amino Acid ◽  
Long Range ◽  
Short Range ◽  
Software Tool ◽  
Contact Networks ◽  
Topological Parameters ◽  
Structure File ◽  
Protein Contact Networks

AMINONETis a Java-based software tool to construct different protein contact networks (unweighted and weighted; long range, short range and any range; hydrophobic, hydrophilic, charged or all-amino-acid networks). The networks thus constructed can be visualized. The software will also help in the calculation of the values of the different topological parameters of the constructed networks. The user can either provide a PDB ID or upload a structure file in PDB format as input. If necessary, the user can also do the same for a large number of proteins, uploading a batch file as input (details described in the document available online).

scholarly journals HiCEnterprise: identifying long range chromosomal contacts in Hi-C data

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10558
Author(s):  
Hanna Kranas ◽  
Irina Tuszynska ◽  
Bartek Wilczynski
Keyword(s):  
Long Range ◽  
Short Range ◽  
Computational Analysis ◽  
Statistical Tests ◽  
Software Tool ◽  
Research Community ◽  
Supplementary Information ◽  
Chromosome Domains ◽  
Growing Body ◽  
Contact Data

Motivation Computational analysis of chromosomal contact data is currently gaining popularity with the rapid advance in experimental techniques providing access to a growing body of data. An important problem in this area is the identification of long range contacts between distinct chromatin regions. Such loops were shown to exist at different scales, either mediating relatively short range interactions between enhancers and promoters or providing interactions between much larger, distant chromosome domains. A proper statistical analysis as well as availability to a wide research community are crucial in a tool for this task. Results We present HiCEnterprise, a first freely available software tool for identification of long range chromatin contacts not only between small regions, but also between chromosomal domains. It implements four different statistical tests for identification of significant contacts for user defined regions or domains as well as necessary functions for input, output and visualization of chromosome contacts. Availability The software and the corresponding documentation are available at: github.com/regulomics/HiCEnterprise. Supplementary information Supplemental data are available in the online version of the article and at the website regulomics.mimuw.edu.pl/wp/hicenterprise.

scholarly journals Structural basis of long-range to short-range synaptic transition in NHEJ

Nature ◽  
2021 ◽  
Author(s):  
Siyu Chen ◽  
Linda Lee ◽  
Tasmin Naila ◽  
Susan Fishbain ◽  
Annie Wang ◽  
...  
Keyword(s):  
Long Range ◽  
Short Range ◽  
Structural Basis

scholarly journals Comparison of short-range order in irradiated dysprosium titanates

2021 ◽  
Vol 5 (1) ◽  
Author(s):  
Roman Sherrod ◽  
Eric C. O’Quinn ◽  
Igor M. Gussev ◽  
Cale Overstreet ◽  
Joerg Neuefeind ◽  
...  
Keyword(s):  
Long Range ◽  
Short Range ◽  
Structural Model ◽  
Ion Irradiation ◽  
Function Analysis ◽  
Ion Beam ◽  
Structural Response ◽  
Heavy Ion ◽  
Range Order ◽  
Radiation Resistant

AbstractThe structural response of Dy2TiO5 oxide under swift heavy ion irradiation (2.2 GeV Au ions) was studied over a range of structural length scales utilizing neutron total scattering experiments. Refinement of diffraction data confirms that the long-range orthorhombic structure is susceptible to ion beam-induced amorphization with limited crystalline fraction remaining after irradiation to 8 × 1012 ions/cm2. In contrast, the local atomic arrangement, examined through pair distribution function analysis, shows only subtle changes after irradiation and is still described best by the original orthorhombic structural model. A comparison to Dy2Ti2O7 pyrochlore oxide under the same irradiation conditions reveals a different behavior: while the dysprosium titanate pyrochlore is more radiation resistant over the long-range with smaller degree of amorphization as compared to Dy2TiO5, the former involves more local atomic rearrangements, best described by a pyrochlore-to-weberite-type transformation. These results highlight the importance of short-range and medium-range order analysis for a comprehensive description of radiation behavior.

SHORT-RANGE AND LONG-RANGE ORDER OF TITANIUM IN Ti1+xS2

1977 ◽  
Vol 38 (C7) ◽  
pp. C7-202-C7-206 ◽  
Author(s):  
R. MORET ◽  
M. HUBER ◽  
R. COMÈS
Keyword(s):  
Long Range ◽  
Short Range ◽  
Range Order ◽  
Long Range Order

scholarly journals Short range smectic order driving long range nematic order: example of cuprates

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
R. S. Markiewicz ◽  
J. Lorenzana ◽  
G. Seibold ◽  
A. Bansil
Keyword(s):  
Long Range ◽  
Short Range ◽  
Nematic Order

ANDERSON LOCALIZATION FOR A MULTIDIMENSIONAL MODEL INCLUDING LONG RANGE POTENTIALS AND DISPLACEMENTS

2002 ◽  
Vol 14 (03) ◽  
pp. 273-302 ◽  
Author(s):  
HERIBERT ZENK
Keyword(s):  
Long Range ◽  
Anderson Model ◽  
Anderson Localization ◽  
Short Range ◽  
Energy Interval ◽  
Multidimensional Model ◽  
Short Summary

We give a short summary on how to combine and extend results of Combes and Hislop [2] (short range Anderson model with additional displacements), Kirsch, Stollmann and Stolz [13] and [14] (long range Anderson model without displacements) to get localization in an energy interval above the infimum of the almost sure spectrum for a continuous multidimensional Anderson model including long range potentials and displacements.

Study on the relationships of mechanical performance with the short-range and long-range structure of 500–900℃ carbonized fiber

2014 ◽  
Vol 45 (1) ◽  
pp. 33-47 ◽  
Author(s):  
Xue Lin ◽  
Chengguo Wang ◽  
Meijie Yu ◽  
Zhitao Lin ◽  
Yuzhen Liu
Keyword(s):  
Long Range ◽  
Short Range ◽  
Mechanical Performance
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