iCn3D, a web-based 3D viewer for sharing 1D/2D/3D representations of biomolecular structures.
Bioinformatics
; 36(1): 131-135, 2020 01 01.
Article
em En
| MEDLINE
| ID: mdl-31218344
ABSTRACT
MOTIVATION Build a web-based 3D molecular structure viewer focusing on interactive structural analysis. RESULTS:
iCn3D (I-see-in-3D) can simultaneously show 3D structure, 2D molecular contacts and 1D protein and nucleotide sequences through an integrated sequence/annotation browser. Pre-defined and arbitrary molecular features can be selected in any of the 1D/2D/3D windows as sets of residues and these selections are synchronized dynamically in all displays. Biological annotations such as protein domains, single nucleotide variations, etc. can be shown as tracks in the 1D sequence/annotation browser. These customized displays can be shared with colleagues or publishers via a simple URL. iCn3D can display structure-structure alignments obtained from NCBI's VAST+ service. It can also display the alignment of a sequence with a structure as identified by BLAST, and thus relate 3D structure to a large fraction of all known proteins. iCn3D can also display electron density maps or electron microscopy (EM) density maps, and export files for 3D printing. The following example URL exemplifies some of the 1D/2D/3D representations https//www.ncbi.nlm.nih.gov/Structure/icn3d/full.html?mmdbid=1TUP&showanno=1&show2d=1&showsets=1. AVAILABILITY AND IMPLEMENTATION iCn3D is freely available to the public. Its source code is available at https//github.com/ncbi/icn3d. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Software
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Sequência de Bases
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Proteínas
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Modelos Moleculares
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Biologia Computacional
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Internet
Idioma:
En
Revista:
Bioinformatics
Assunto da revista:
INFORMATICA MEDICA
Ano de publicação:
2020
Tipo de documento:
Article
País de afiliação:
Estados Unidos