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Titolo:
Bridging the information gap: Computational tools for intermediate resolution structure interpretation
Autore:
Jiang, W; Baker, ML; Ludtke, SJ; Chiu, W;
Indirizzi:
Baylor Coll Med, Program Struct & Computat Biol & Mol Biophys, Houston, TX77030 USA Baylor Coll Med Houston TX USA 77030 & Mol Biophys, Houston, TX77030 USA Baylor Coll Med, Verna & Marrs McLean Dept Biochem & Mol Biol, Houston, TX77030 USA Baylor Coll Med Houston TX USA 77030 hem & Mol Biol, Houston, TX77030 USA
Titolo Testata:
JOURNAL OF MOLECULAR BIOLOGY
fascicolo: 5, volume: 308, anno: 2001,
pagine: 1033 - 1044
SICI:
0022-2836(20010518)308:5<1033:BTIGCT>2.0.ZU;2-N
Fonte:
ISI
Lingua:
ENG
Soggetto:
LARGE RIBOSOMAL-SUBUNIT; BLUETONGUE VIRUS VP7; ANGSTROM RESOLUTION; CRYSTAL-STRUCTURE; CRYOELECTRON MICROSCOPY; PROTEIN; ELEMENTS; DATABASE; DOMAIN; FOLD;
Keywords:
macromolecular assemblies; structure; fold recognition; electron cryomicroscopy; bioinformatics;
Tipo documento:
Article
Natura:
Periodico
Settore Disciplinare:
Life Sciences
Citazioni:
34
Recensione:
Indirizzi per estratti:
Indirizzo: Chiu, W Baylor Coll Med, Program Struct & Computat Biol & Mol Biophys, Houston, TX77030 USA Baylor Coll Med Houston TX USA 77030 iophys, Houston, TX77030 USA
Citazione:
W. Jiang et al., "Bridging the information gap: Computational tools for intermediate resolution structure interpretation", J MOL BIOL, 308(5), 2001, pp. 1033-1044

Abstract

Due to large sizes and complex nature, few large macromolecular complexes have been solved to atomic resolution. This has lead to an under-representation of these structures, which are composed of novel and/or homologous folds, in the library of known structures and folds. While it is often difficult to achieve a high-resolution model for these structures, X-ray crystallography and electron cryomicroscopy are capable of determining structures oflarge assemblies at low to intermediate resolutions. To aid in the interpretation and analysis of such structures, we have developed two programs: helixhunter and foldhunter. Helixhunter is capable of reliably identifying helix position, orientation and length using a five-dimensional cross-correlation search of a three-dimensional density map followed by feature extraction. Helixhunter's results can in turn be used to probe a library of secondary structure elements derived from the structures in the Protein Data Bank (PDB). From this analysis, it is then possible to identify potential homologous folds or suggest novel folds based on the arrangement of alpha helix elements, resulting in a structure-based recognition of folds containing alpha helices. Foldhunter uses a six-dimensional cross-correlation search allowing a probe structure to be fitted within a region or component of a target structure. The structural fitting therefore provides a quantitative meansto further examine the architecture and organization of large, complex assemblies. These two methods have been successfully tested with simulated structures modeled from the PDB at resolutions between 6 and 12 Angstrom. Withthe integration of helixhunter and foldhunter into sequence and structuralinformatics techniques, we have the potential to deduce or confirm known or novel folds in domains or components within large complexes. (C) 2001 Academic Press.

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Documento generato il 19/01/20 alle ore 21:05:30