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Archer : predicting protein function using local structural features. A helpful tool for protein redesign
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Bonet, Jaume, Garcia-Garcia, Javier, Planas-Iglesias, Joan, Fernandez-Fuentes, Narcis and Oliva, Baldo (2015) Archer : predicting protein function using local structural features. A helpful tool for protein redesign. In: 29th Annual Symposium of the Protein-Society, Barcelona, Spain, 22nd-25th July 2015. Published in: Protein Science, 24 p. 221. ISSN 0961-8368.
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Abstract
The advance of high-throughput sequencing methodologies has led to an exponential increase of new protein sequences, a large proportion of which remain unannotated. The gap between the number of known proteins and those with assigned function is increasing. In light of this situation, computational methods to predict the function of proteins have become a valid and necessary strategy. Here we pres- ent Archer, a server that exploits ArchDB’s hierarchy of super-secondary structures to map GO and Enzyme functions upon protein regions and, thus, infer the function of a protein. The server relies on either the sequence or structure of the protein of interest and returns the mapping of functional sub- classes extracted from ArchDB. Moreover, it computes the functional enrichment and significance of each subclass, combines the functional descriptors and predicts the function of the query-protein. Com- bining the functional enrichment analysis of the super-secondary structures with the structural classifica- tion of ArchDB, users can select variants of the target sequence that swap the region of a super- secondary structure by another that putatively fits in the same scaffold minimizing the effect on the global tertiary structure. Only variants that modify the predicted function are offered for selection, thus providing a rational, knowledge-based, approach for protein design and functionalization. The Archer server is accessible at http://sbi.imim.es/archer.
Item Type: | Conference Item (Paper) | ||||
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Divisions: | Faculty of Science, Engineering and Medicine > Medicine > Warwick Medical School > Biomedical Sciences > Translational & Experimental Medicine > Metabolic and Vascular Health (- until July 2016) Faculty of Science, Engineering and Medicine > Medicine > Warwick Medical School |
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Journal or Publication Title: | Protein Science | ||||
Publisher: | John Wiley & Sons Ltd. | ||||
ISSN: | 0961-8368 | ||||
Official Date: | 2015 | ||||
Dates: |
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Volume: | 24 | ||||
Page Range: | p. 221 | ||||
Status: | Peer Reviewed | ||||
Publication Status: | Published | ||||
Access rights to Published version: | Restricted or Subscription Access | ||||
Conference Paper Type: | Paper | ||||
Title of Event: | 29th Annual Symposium of the Protein-Society | ||||
Type of Event: | Conference | ||||
Location of Event: | Barcelona, Spain | ||||
Date(s) of Event: | 22nd-25th July 2015 |
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