Domain fishing: a first step in protein comparative modelling
B Contreras-Moreira, PA Bates - Bioinformatics, 2002 - academic.oup.com
Bioinformatics, 2002•academic.oup.com
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@ cancer. org. uk paul. bates@ cancer. org. uk
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@ cancer. org. uk paul. bates@ cancer. org. uk
Abstract
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@cancer.org.ukpaul.bates@cancer.org.uk
Oxford University Press