Bioinformatics Vol. 18 no. 8 2002
Pages 1141-1142
© 2002 Oxford University Press
Applications Note |
Domain Fishing: a first step in protein comparative modelling
Biomolecular Modelling Laboratory, Cancer Research UK London Research Institute, Lincoln's Inn Fields Laboratories, 44 Lincoln's Inn Fields, London WC2A 3PX, UK
Received on January 17, 2002
; revised on February 27, 2002
; accepted on March 11, 2002
Summary: To optimize the search for structural templates in protein comparative modelling, the query sequence is split into domains. The initial list of templates for each domain, extracted from PFAM plus PDB and SCOP, is then ranked according to sequence identity (%ID), coverage and resolution. If %ID is less than 30, secondary structure matching is used to filter out false templates.
Availability: http://www.bmm.icnet.uk/~3djigsaw/dom_fish
Contact: b.contreras-moreira{at}cancer.org.uk paul.bates{at}cancer.org.uk
* To whom correspondence should be addressed.
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