Automated main-chain model building by template matching and iterative fragment extension
- Mail Stop M888, Los Alamos National Laboratory, Los Alamos, NM 87545 (United States)
A method for automated macromolecular main-chain model building is described. An algorithm for the automated macromolecular model building of polypeptide backbones is described. The procedure is hierarchical. In the initial stages, many overlapping polypeptide fragments are built. In subsequent stages, the fragments are extended and then connected. Identification of the locations of helical and β-strand regions is carried out by FFT-based template matching. Fragment libraries of helices and β-strands from refined protein structures are then positioned at the potential locations of helices and strands and the longest segments that fit the electron-density map are chosen. The helices and strands are then extended using fragment libraries consisting of sequences three amino acids long derived from refined protein structures. The resulting segments of polypeptide chain are then connected by choosing those which overlap at two or more C{sup α} positions. The fully automated procedure has been implemented in RESOLVE and is capable of model building at resolutions as low as 3.5 Å. The algorithm is useful for building a preliminary main-chain model that can serve as a basis for refinement and side-chain addition.
- OSTI ID:
- 22347955
- Journal Information:
- Acta Crystallographica. Section D: Biological Crystallography, Vol. 59, Issue Pt 1; Other Information: PMCID: PMC2745878; PMID: 12499537; PUBLISHER-ID: gr2291; OAI: oai:pubmedcentral.nih.gov:2745878; Copyright (c) International Union of Crystallography 2003; This is an open-access article distributed under the terms described at http://journals.iucr.org/services/termsofuse.html.; Country of input: International Atomic Energy Agency (IAEA); ISSN 0907-4449
- Country of Publication:
- Denmark
- Language:
- English
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