2017
DOI: 10.1126/sciadv.1600552
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An ambiguity principle for assigning protein structural domains

Abstract: Our novel algorithm for delimiting protein structural domains provides insights into protein folding, function, and evolution.

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Cited by 40 publications
(58 citation statements)
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“…Presence of multiple domains in proteins has been reported to confer structural stability [6] and folding and functional advantages [7]. Proteins can be decomposed into domains based on various criteria namely sequence, structure, function, evolution and mobility [8,9]. At the sequence level, domains are defined on the basis of conservation of residues over significant length; structural domains are defined on the basis of globularity and compactness; functional domains are modules in proteins which can function independently of other modules in the protein; evolutionary domains are protein modules propagating through evolution by recombination, transposition, shuffling etc.…”
mentioning
confidence: 99%
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“…Presence of multiple domains in proteins has been reported to confer structural stability [6] and folding and functional advantages [7]. Proteins can be decomposed into domains based on various criteria namely sequence, structure, function, evolution and mobility [8,9]. At the sequence level, domains are defined on the basis of conservation of residues over significant length; structural domains are defined on the basis of globularity and compactness; functional domains are modules in proteins which can function independently of other modules in the protein; evolutionary domains are protein modules propagating through evolution by recombination, transposition, shuffling etc.…”
mentioning
confidence: 99%
“…and protein modules with high correlated mobility are identified as domains according to the mobility definition [8]. It is important to note that a given protein may have different but equally valid domain annotations depending upon the basis of domain annotation [9]. Often domains in multi-domain proteins interact with one another.…”
mentioning
confidence: 99%
“…Even when experimental atomic resolution structures are available, the process of defining the boundaries of a protein fragment that can fold independently remains ambiguous, with algorithms based on dynamic, evolutionary, functional, geometric or thermodynamic definitions of a domain yielding conflicting results 18 . The task is more difficult still if the boundaries must be parsed from sequence information alone, for example when designing expression constructs for portions of a multi-domain protein to facilitate structural studies.…”
Section: Discussionmentioning
confidence: 99%
“…SWORD provides different domain assignments using different merge schemes. 2017 www.dsimb.inserm.fr/sword/ [53] Predcitedstructure-based SnapDRAGON DRAGON generates 100 models, and then structure-based domain assignment is used to parse the models into domains. Finally, a result is derived from the consistency of the predicted boundaries.…”
Section: Protein Domain Detection Methodsmentioning
confidence: 99%
“…Therefore, some proteins will be decomposed into different domains using different tools. Considering that a protein may be divided into different but equally valid domain, SWORD [53] was developed to generate multiple alternative domain architectures for a target protein. It defines protein units (PUs), a structural descriptor between secondary structures and domains.…”
Section: Protein Domain Detection Methodsmentioning
confidence: 99%