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Curves+ specifications

Information


Unique identifier OMICS_03582
Name Curves+
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for Curves+

Curves+ citations

 (106)
library_books

Structural basis of DNA target recognition by the B3 domain of Arabidopsis epigenome reader VAL1

2018
Nucleic Acids Res
PMCID: 5934628
PMID: 29660015
DOI: 10.1093/nar/gky256

[…] n domains of restriction endonucleases EcoRII, BfiI, NgoAVII and UbaLAI ()). Like the above proteins, VAL1-B3 does not distort the DNA. The overall bend for the 12 bp oligoduplex, as determine by the Curves+ web server (), is only ∼5° (); in comparison, the DNA fragment directly interacting with ARF1-B3 (PDB ID: 4ldx) is also bent by ∼3–5°, albeit the overall DNA axis direction relative to the pro […]

call_split

Probing the role of intercalating protein sidechains for kink formation in DNA

2018
PLoS One
PMCID: 5809078
PMID: 29432448
DOI: 10.1371/journal.pone.0192605
call_split See protocol

[…] ase (NDB) [, ] containing a total of 8617 protein DNA complexes (accessed June 2016). Only crystal structures containing B-DNA segments were considered for further analysis of their roll angles using Curves+ []. The strategy, which is described in detail in the results section and in , resulted in a total of 88 kinked DNA-structures for 15 different types of protein-DNA complexes.From these 15 sys […]

library_books

A systematic analysis of nucleosome core particle and nucleosome nucleosome stacking structure

2018
Sci Rep
PMCID: 5784010
PMID: 29367745
DOI: 10.1038/s41598-018-19875-0

[…] e-written Fortran scripts. The Chimera software was used to build molecular structures and surfaces and to create figures. Structural parameters of the NCP double stranded (ds) DNA were calculated by Curves+,. Parameters of the DNA superhelix (radius, pitch, number of DNA base pairs in one turn, dyad axis) were determined using coordinates of the 129 central dsDNA axis points (of total 145–147 bp) […]

library_books

Two distinct DNA sequences recognized by transcription factors represent enthalpy and entropy optima

2018
eLife
PMCID: 5896879
PMID: 29638214
DOI: 10.7554/eLife.32963.032

[…] supplement 1. 10.7554/eLife.32963.008 Figure 2—figure supplement 2. To quantitate the shape of the DNA in the protein binding region we determined the helicoidal parameters using the program Curves+ (), and found that the most prominent differences between the two complexes were in twist, shift, slide, X- and Y-displacement, minor groove width, and major groove depth at the positions of t […]

library_books

Sequence dependent response of DNA to torsional stress: a potential biological regulation mechanism

2017
Nucleic Acids Res
PMCID: 5829783
PMID: 29267977
DOI: 10.1093/nar/gkx1270

[…] may play an important role in how DNA reacts to torsional strain and the aim of this study is to address this question.In order to do this, we have developed a new structural constraint, based on the Curves+ conformational analysis methodology (), which controls the total helical twist between two chosen base pairs, allowing both under- and overtwisting to be imposed. This restraint has been imple […]

library_books

Molecular dynamics simulations of the glucocorticoid receptor DNA binding domain suggest a role of the lever arm mobility in transcriptional output

2017
PLoS One
PMCID: 5731742
PMID: 29244866
DOI: 10.1371/journal.pone.0189588

[…] of communication flow between communities was quantified by the total betweenness of all edges that transition between communities. Geometric DNA analysis and base pair parameters were obtained using Curves+ [] and Canal utility. […]

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Curves+ institution(s)
Institut de Biologie et Chimie des Protéines, CNRS UMR 5086/Université de Lyon, Lyon, France

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