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NUCPLOT specifications

Information


Unique identifier OMICS_03583
Name NUCPLOT
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for NUCPLOT

NUCPLOT in publications

 (23)
PMCID: 5871717
PMID: 29551265
DOI: 10.1016/j.cell.2018.02.032

[…] figures and animations were generated with pymol (schrödinger); sequence alignments were generated with dali () and espript (). protein interfaces were analyzed in pisa (), protein-dna contacts in nucplot () and dna parameters in 3dna ()., reaction products from strand exchange assays with int82n, r153a, and r153a-y160a mutants were quantified using a typhoon fla7000 phosphorimager […]

PMCID: 5766154
PMID: 28934482
DOI: 10.1093/nar/gkx624

[…] from the dna binding (). there are at least 10 hydrogen bonds and multiple van der waals interactions involved in the formation of the ader_dbd/dna complex. the detailed interaction was plotted with nucplot as shown in figure (). the nh2 groups from positive residues such as arg205, arg215, arg231 and the oh group from tyr235, the og group from ser209, ser212 and thr171 form hydrogen bonds […]

PMCID: 5389614
PMID: 28039325
DOI: 10.1093/nar/gkw1310

[…] in parenthesis., the contact surfaces buried between the two molecules were calculated using pisa server (http://www.ebi.ac.uk/pdbe/prot_int/pistart.html) (). protein–dna contacts were analyzed by nucplot (). all molecular scale representations were prepared using molscript () and raster3d () software., dna duplex sp () and his-agei were used for gel filtration. gel filtration was carried […]

PMCID: 5224481
PMID: 27899589
DOI: 10.1093/nar/gkw1113

[…] the inclusion of low-resolution data and bulk solvent correction, the final r/rfree values were 15.5/20.8 for terδt3 and 20.8/26.8 for terδt12. the structures were analyzed using molprobity () and nucplot (). a summary of refinement statistics is show in supplementary table s1. molecular graphics figures were prepared with pymol (delano scientific, palo alto, ca, usa)., binding energies […]

PMCID: 4824133
PMID: 27110240
DOI: 10.1155/2016/8792814

[…] 1 and s1). most of the complexes are held stable by several strong h-bonding interactions (about 25 to 40) of distance less than 3 å. a 2d representation of ago2-sirna interactions is analyzed using nucplot software [] and the observed interactions are depicted in supplementary figure 4. lists the existing strong interactions between human ago2 and sirnas, which are mandatory for efficient […]


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NUCPLOT institution(s)
Biomolecular Structure and Modelling Unit, Department of Biochemistry and Molecular Biology, University College, Gower Street, London, UK

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