NanoTiler protocols

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NanoTiler specifications

Information


Unique identifier OMICS_10685
Name NanoTiler
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java
Computer skills Medium
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Bruce Shapiro <>

Publication for NanoTiler

NanoTiler in pipeline

2010
PMCID: 2934861
PMID: 20802494
DOI: 10.1038/nnano.2010.160

[…] number of possible functions within each scaffold is at least as large as the number of addressable nucleic acid units present in its composition., computational 3d models were generated using the nanotiler software as well as accelrys discovery studio. the computational sequence optimization consists of sequence randomization and monte carlo optimization algorithms (). the objective function […]


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NanoTiler in publications

 (7)
PMCID: 5389727
PMID: 28108656
DOI: 10.1093/nar/gkx008

[…] were performed for the different combinations of rna and dna strands using new hyperfold. the rna, rna/dna and dna cube models were built using pymol. the triangle models were built with the aid of nanotiler (https://binkley2.ncifcrf.gov/users/bshapiro/software.html)., to determine the re-association of nanoparticles in vitro, fret measurements were performed using a fluoromax3 (jobin-yvon, […]

PMCID: 5333189
PMID: 28045501
DOI: 10.1021/acsnano.6b05737

[…] from trna (b-i) and nanoprisms designed from prna (b-ii).,,,,− (6) construction of rna nanoparticles via computational design. several software programs have been developed over the years, such as nanotiler, assemble2, rna2d3d, info-rna, and nupack, which are useful to design de novo rna nanoparticles. examples are a six-membered rna nanoring and an rna nanocube generated using nanotiler (c). […]

PMCID: 4707685
PMID: 26770259
DOI: 10.1016/j.nantod.2015.09.003

[…] rna folding program developed by zuker 30 years ago []. it is expected that computer algorithms will facilitate rna nanoparticle construction. a variety of computer programs such as nanofolder, nanotiler and rna2d3d are available to facilitate the in silico design of rna sequences (these sequences may contain inter-strand and intra-strand pseudoknot-like interactions) capable […]

PMCID: 4189619
PMID: 25267559
DOI: 10.1021/nl502385k

[…] the map was deposited to emdb (emd-2783)., models of hexmeric nanorings with six ds sirna arms were created by merging the model of the hexameric ring scaffold, built with the aid of our program nanotiler (http://www.lecb.ncifcrf.gov/bshapiro/software.html) with several alternative models of one monomer with the sirna arm. monomer models were built with the aid of programs rna2d3d […]

PMCID: 4066900
PMID: 24758371
DOI: 10.1021/ar400329z

[…] for use by programs that optimize the sequence or sequences guaranteeing their correct self-assembly (figure d,e)., while there are a variety of rna 3d modeling programs,, we mostly use our nanotiler and rna2d3d programs for nanostructure modeling (figures )., the user can interact with nanotiler via a graphical interface (figure a) or scripting language., one of the capabilities […]


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NanoTiler institution(s)
Basic Science Program, SAIC-Frederick, Inc, NCI at Frederick, Frederick, MD, USA; Center for Cancer Research Nanobiology Program, National Cancer Institute at Frederick, Frederick, MD, USA

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