Academic Journal

iCn3D, a web-based 3D viewer for sharing 1D/2D/3D representations of biomolecular structures

التفاصيل البيبلوغرافية
العنوان: iCn3D, a web-based 3D viewer for sharing 1D/2D/3D representations of biomolecular structures
المؤلفون: Wang, Jiyao, Youkharibache, Philippe, Zhang, Dachuan, Lanczycki, Christopher J, Geer, Renata C, Madej, Thomas, Phan, Lon, Ward, Minghong, Lu, Shennan, Marchler, Gabriele H, Wang, Yanli, Bryant, Stephen H, Geer, Lewis Y, Marchler-Bauer, Aron
المساهمون: Valencia, Alfonso, the Intramural Research Program, National Library of Medicine, National Institutes of Health, DHHS
المصدر: Bioinformatics ; volume 36, issue 1, page 131-135 ; ISSN 1367-4803 1367-4811
بيانات النشر: Oxford University Press (OUP)
سنة النشر: 2019
الوصف: 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.
نوع الوثيقة: article in journal/newspaper
اللغة: English
DOI: 10.1093/bioinformatics/btz502
DOI: 10.1093/bioinformatics/btz502/29185120/btz502.pdf
الاتاحة: http://dx.doi.org/10.1093/bioinformatics/btz502
http://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btz502/29185120/btz502.pdf
https://academic.oup.com/bioinformatics/article-pdf/36/1/131/48981423/bioinformatics_36_1_131.pdf
Rights: https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model
رقم الانضمام: edsbas.9021FC9D
قاعدة البيانات: BASE
الوصف
DOI:10.1093/bioinformatics/btz502