Investigating Molecular Recognition Through Large-scale Analysis of Protein Sequences and Structures

2000 ◽  
Author(s):  
Mark Gerstein
Keyword(s):  
Molecular Recognition ◽  
Large Scale ◽  
Protein Sequences ◽  
Scale Analysis ◽  
Large Scale Analysis

In search of the boundary between repetitive and non-repetitive protein sequences

2015 ◽  
Vol 43 (5) ◽  
pp. 807-811 ◽  
Author(s):  
François D. Richard ◽  
Andrey V. Kajava
Keyword(s):  
Large Scale ◽  
Tandem Repeats ◽  
Protein Sequences ◽  
Scoring Functions ◽  
Scale Analysis ◽  
3D Structures ◽  
Large Scale Analysis ◽  
Repetitive Protein

Tandem repeats (TRs) are frequently not perfect, containing a number of mutations accumulated during evolution. One of the main problems is to distinguish between the sequences that contain highly imperfect TRs and the aperiodic sequences. The majority of proteins with TRs in sequences have repetitive arrangements in their 3D structures. Therefore, the 3D structures of proteins can be used as a benchmarking criterion for TR detection in sequences. Different TR detection tools use their own scoring procedures to determine the boundary between repetitive and non-repetitive protein sequences. Here we described these scoring functions and benchmark them by using known structural TRs. Our survey shows that none of the existing scoring procedures are able to achieve an appropriate separation between genuine structural TRs and non-TR regions. This suggests that if we want to obtain a collection of structurally and functionally meaningful TRs from a large scale analysis of proteomes, the TR scoring metrics need to be improved.

scholarly journals Large-scale analysis of conserved rare codon clusters suggests an involvement in co-translational molecular recognition events

2012 ◽  
Vol 28 (11) ◽  
pp. 1438-1445 ◽  
Author(s):  
Matthieu Chartier ◽  
Francis Gaudreault ◽  
Rafael Najmanovich
Keyword(s):  
Molecular Recognition ◽  
Large Scale ◽  
Rare Codon ◽  
Scale Analysis ◽  
Large Scale Analysis

scholarly journals Identifying draught cattle in the past: Lessons from large-scale analysis of archaeological datasets

2021 ◽  
Vol 33 ◽  
pp. 258-269
Author(s):  
Matilda Holmes ◽  
Richard Thomas ◽  
Helena Hamerow
Keyword(s):  
Large Scale ◽  
Scale Analysis ◽  
The Past ◽  
Large Scale Analysis

scholarly journals Advances in decomposing complex metabolite mixtures using substructure- and network-based computational metabolomics approaches

2021 ◽  
Author(s):  
Mehdi A. Beniddir ◽  
Kyo Bin Kang ◽  
Grégory Genta-Jouve ◽  
Florian Huber ◽  
Simon Rogers ◽  
...  
Keyword(s):  
Natural Product ◽  
Large Scale ◽  
Scale Analysis ◽  
Computational Tools ◽  
Natural Product Discovery ◽  
Large Scale Analysis ◽  
Metabolite Annotation

This review highlights the key computational tools and emerging strategies for metabolite annotation, and discusses how these advances will enable integrated large-scale analysis to accelerate natural product discovery.

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