| Nucleic acid visualization with UCSF Chimera. | |
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MedLine Citation:
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PMID: 16478715 Owner: NLM Status: MEDLINE |
Abstract/OtherAbstract:
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With the increase in the number of large, 3D, high-resolution nucleic acid structures, particularly of the 30S and 50S ribosomal subunits and the intact bacterial ribosome, advancements in the visualization of nucleic acid structural features are essential. Large molecular structures are complicated and detailed, and one goal of visualization software is to allow the user to simplify the display of some features and accent others. We describe an extension to the UCSF Chimera molecular visualization system for the purpose of displaying and highlighting nucleic acid characteristics, including a new representation of sugar pucker, several options for abstraction of base geometries that emphasize stacking and base pairing, and an adaptation of the ribbon backbone to accommodate the nucleic acid backbone. Molecules are displayed and manipulated interactively, allowing the user to change the representations as desired for small molecules, proteins and nucleic acids. This software is available as part of the UCSF Chimera molecular visualization system and thus is integrated with a suite of existing tools for molecular graphics. |
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Authors:
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Gregory S Couch; Donna K Hendrix; Thomas E Ferrin |
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Publication Detail:
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Type: Journal Article; Research Support, N.I.H., Extramural Date: 2006-02-14 |
Journal Detail:
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Title: Nucleic acids research Volume: 34 ISSN: 1362-4962 ISO Abbreviation: Nucleic Acids Res. Publication Date: 2006 |
Date Detail:
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Created Date: 2006-02-15 Completed Date: 2006-02-28 Revised Date: 2009-11-18 |
Medline Journal Info:
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Nlm Unique ID: 0411011 Medline TA: Nucleic Acids Res Country: England |
Other Details:
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Languages: eng Pagination: e29 Citation Subset: IM |
Affiliation:
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Computer Graphics Laboratory, Department of Pharmaceutical Chemistry, University of California, 600 16th Street, San Francisco, CA 94143-2240, USA. |
Export Citation:
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APA/MLA Format Download EndNote Download BibTex |
| MeSH Terms | |
Descriptor/Qualifier:
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Base Pairing Carbohydrates / chemistry Computer Graphics* DNA / chemistry Internet Models, Molecular* Nucleic Acid Conformation* RNA / chemistry Software* |
| Grant Support | |
ID/Acronym/Agency:
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P41 RR001081/RR/NCRR NIH HHS; R01 GM066199/GM/NIGMS NIH HHS |
| Chemical | |
Reg. No./Substance:
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0/Carbohydrates; 63231-63-0/RNA; 9007-49-2/DNA |
| Comments/Corrections | |
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
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