Protein structure prediction on the Web: a case study using the Phyre server View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2009-03

AUTHORS

Lawrence A Kelley, Michael J E Sternberg

ABSTRACT

Determining the structure and function of a novel protein is a cornerstone of many aspects of modern biology. Over the past decades, a number of computational tools for structure prediction have been developed. It is critical that the biological community is aware of such tools and is able to interpret their results in an informed way. This protocol provides a guide to interpreting the output of structure prediction servers in general and one such tool in particular, the protein homology/analogy recognition engine (Phyre). New profile-profile matching algorithms have improved structure prediction considerably in recent years. Although the performance of Phyre is typical of many structure prediction systems using such algorithms, all these systems can reliably detect up to twice as many remote homologies as standard sequence-profile searching. Phyre is widely used by the biological community, with >150 submissions per day, and provides a simple interface to results. Phyre takes 30 min to predict the structure of a 250-residue protein. More... »

PAGES

363-371

References to SciGraph publications

Identifiers

URI

http://scigraph.springernature.com/pub.10.1038/nprot.2009.2

DOI

http://dx.doi.org/10.1038/nprot.2009.2

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1029454980

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/19247286


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