iCn3D, a Web-based 3D Viewer for Sharing 1D/2D/3D Representations of Biomolecular Structures
| Autor: | Stephen H. Bryant, Dachuan Zhang, Yanli Wang, Philippe Youkharibache, Renata C. Geer, Christopher J. Lanczycki, Gabriele H. Marchler, Lewis Y. Geer, Jiyao Wang, Lon Phan, Shennan Lu, Thomas Madej, Minghong Ward, Aron Marchler-Bauer |
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| Rok vydání: | 2018 |
| Předmět: |
Statistics and Probability
Models Molecular Source code Computer science media_common.quotation_subject Protein domain Molecular Conformation Biochemistry Molecular conformation 03 medical and health sciences 0302 clinical medicine Simple (abstract algebra) Databases Genetic Web application Nucleotide Molecular Biology 030304 developmental biology media_common Structure (mathematical logic) chemistry.chemical_classification 0303 health sciences Internet Sequence Information retrieval Base Sequence business.industry Computational Biology Proteins Original Papers Computer Science Applications Computational Mathematics Computational Theory and Mathematics chemistry business 030217 neurology & neurosurgery Software |
| DOI: | 10.1101/501692 |
| Popis: | SummaryiCn3D (I-see-in-3D) is a web-based 3D molecular structure viewer focusing on the interactive structural analysis. It 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 alignment 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 implementationiCn3D is freely available to the public. Its source code is available at https://github.com/ncbi/icn3d.Supplementary informationUser instructions are available at Bioinformatics online |
| Databáze: | OpenAIRE |
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