title: Dynamic domain threading.
abstract: A modeling method is described that avoids the need to consider the domain structure of the template used for modeling, and automatically extracts compact fragments of structure that would be of a suitable size to build the model. This aids automation as the size or nature of the template structure can be ignored and does not have to be broken into domain (or multi-domain) units beforehand. The approach leads to the generation of a large number of models each based on slightly differing domain definitions and this variation was further increased by considering alternative secondary structure predictions. Each model, of which there may be thousands, takes the form of a complete alpha-carbon trace and some methods (including residue burial) were investigated for their power to discriminate good models from bad models using decoys. The method is also compared to an earlier retroviral capsid modeling problem for which the X-ray structure is now known. Some potential extensions of the approach to more distant modeling problems are discussed.
authors.affiliation: Division of Mathematical Biology, National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, United Kingdom. wtaylor@nimr.mrc.ac.uk
authors.forename: William R
authors.initials: WR
authors.lastname: Taylor
authors.forename: Kuang
authors.initials: K
authors.lastname: Lin
authors.forename: Daniel
authors.initials: D
authors.lastname: Klose
authors.forename: Franca
authors.initials: F
authors.lastname: Fraternali
authors.forename: Inge
authors.initials: I
authors.lastname: Jonassen
mesh_terms: D000465:Algorithms; D019295:Computational Biology; D030562:Databases, Protein; D008958:Models, Molecular; D017510:Protein Folding; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D012191:Retroviridae Proteins / Q000737:chemistry; D016415:Sequence Alignment / Q000379:methods; D012984:Software
chemical_list: D011506:Proteins; D012191:Retroviridae Proteins