scholarly journals RASS: a web server for RNA alignment in the joint sequence-structure space

2014 ◽  
Vol 42 (W1) ◽  
pp. W377-W381 ◽  
Author(s):  
Gewen He ◽  
Albert Steppi ◽  
Jose Laborde ◽  
Anuj Srivastava ◽  
Peixiang Zhao ◽  
...  
Keyword(s):  
Web Server ◽  
Sequence Structure ◽  
Structure Space

Evidence for the Emergence of β-Trefoils by ‘Peptide Budding’ from an IgG-like β-Sandwich

2021 ◽  
Author(s):  
Liam M. Longo ◽  
Rachel Kolodny ◽  
Shawn E. McGlynn
Keyword(s):  
De Novo ◽  
General Trend ◽  
Sequence Structure ◽  
Structure Comparison ◽  
Related Sequence ◽  
Structure Space ◽  
Protein Universe ◽  
Remote Islands ◽  
Comparison Algorithms ◽  
Hallmark Feature

AbstractAs sequence and structure comparison algorithms gain sensitivity, the intrinsic interconnectedness of the protein universe has become increasingly apparent. Despite this general trend, β-trefoils have emerged as an uncommon counterexample: They are an isolated protein lineage for which few, if any, sequence or structure associations to other lineages have been identified. If β-trefoils are, in fact, remote islands in sequence-structure space, it implies that the oligomerizing peptide that founded the β-trefoil lineage itself arose de novo. To better understand β-trefoil evolution, and to probe the limits of fragment sharing across the protein universe, we identified both ‘β-trefoil bridging themes’ (evolutionarily-related sequence segments) and ‘β-trefoil-like motifs’ (structure motifs with a hallmark feature of the β-trefoil architecture) in multiple, ostensibly unrelated, protein lineages. The success of the present approach stems, in part, from considering β-trefoil sequence segments or structure motifs rather than the β-trefoil architecture as a whole, as has been done previously. The newly uncovered inter-lineage connections presented here suggest a novel hypothesis about the origins of the β-trefoil fold itself – namely, that it is a derived fold formed by ‘budding’ from an Immunoglobulin-like β-sandwich protein. These results demonstrate how the emergence of a folded domain from a peptide need not be a signature of antiquity and underpin an emerging truth: few protein lineages escape nature’s sewing table.

scholarly journals RNA global alignment in the joint sequence–structure space using elastic shape analysis

2013 ◽  
Vol 41 (11) ◽  
pp. e114-e114 ◽  
Author(s):  
Jose Laborde ◽  
Daniel Robinson ◽  
Anuj Srivastava ◽  
Eric Klassen ◽  
Jinfeng Zhang
Keyword(s):  
Shape Analysis ◽  
Global Alignment ◽  
Sequence Structure ◽  
Structure Space ◽  
Elastic Shape Analysis

scholarly journals RNAPattMatch: a web server for RNA sequence/structure motif detection based on pattern matching with flexible gaps

2015 ◽  
Vol 43 (W1) ◽  
pp. W507-W512 ◽  
Author(s):  
Matan Drory Retwitzer ◽  
Maya Polishchuk ◽  
Elena Churkin ◽  
Ilona Kifer ◽  
Zohar Yakhini ◽  
...  
Keyword(s):  
Pattern Matching ◽  
Web Server ◽  
Sequence Structure ◽  
Rna Sequence ◽  
Motif Detection

Exploring the extremes of sequence/structure space with ensemble fold recognition in the program Phyre

2008 ◽  
Vol 70 (3) ◽  
pp. 611-625 ◽  
Author(s):  
Riccardo M. Bennett‐Lovsey ◽  
Alex D. Herbert ◽  
Michael J. E. Sternberg ◽  
Lawrence A. Kelley
Keyword(s):  
Fold Recognition ◽  
Sequence Structure ◽  
Structure Space

scholarly journals XSuLT: a web server for structural annotation and representation of sequence-structure alignments

2017 ◽  
Vol 45 (W1) ◽  
pp. W381-W387 ◽  
Author(s):  
Bernardo Ochoa-Montaño ◽  
Tom L. Blundell
Keyword(s):  
Web Server ◽  
Sequence Structure ◽  
Structural Annotation

FACTORS INFLUENCING HOME BUYERS’ PURCHASE DECISIONS IN KLANG VALLEY, MALAYSIA

2020 ◽  
Vol 7 (2) ◽  
pp. 77
Author(s):  
JieSheng Mang ◽  
Rozlin Zainal ◽  
Indera Syahrul Mat Radzuan
Keyword(s):  
Purchase Decision ◽  
Purchase Decisions ◽  
Structure Space ◽  
Factors Influencing ◽  
Klang Valley ◽  
Housing Industry ◽  
House Structure ◽  
Research Studies

Focusing on Klang Valley, this research studies the outcome of house purchase factors in Malaysia. This research identifies the house purchase factors that affect home buyers’ purchase decisions. The researcher collected data using SurveyMonkey by using a questionnaire to elicit the opinions of Klang Valley residents on housing purchase factors and purchase decision. The factors were evaluated and studied to identify their influence on home buyers’ purchase decision. Findings show that home buyers’ purchase decision are influenced by house structure, space, finance, location, and neighbourhood factors. The findings have laid a foundation for the housing industry to improve.

Jurnal uji web serber

2020 ◽  
Author(s):  
Wawan saputra
Keyword(s):  
Web Server ◽  
Word Wide Web

Web server adalah tulang belakang dari word wide web(www)

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