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Dynamic domain threading
Author(s) -
Taylor William R.,
Lin Kuang,
Klose Daniel,
Fraternali Franca,
Jonassen Inge
Publication year - 2006
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.20915
Subject(s) - computer science , threading (protein sequence) , domain (mathematical analysis) , domain model , algorithm , trace (psycholinguistics) , theoretical computer science , protein structure , artificial intelligence , domain knowledge , mathematics , physics , mathematical analysis , linguistics , philosophy , nuclear magnetic resonance
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. Proteins 2006. © 2006 Wiley‐Liss, Inc.