ElNemo protocols

View ElNemo computational protocol

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ElNemo specifications

Information


Unique identifier OMICS_07562
Name ElNemo
Interface Web user interface
Restrictions to use None
Input format PDB
Computer skills Basic
Stability Stable
Maintained Yes

Publications for ElNemo

ElNemo in pipelines

 (2)
2016
PMCID: 5291275
PMID: 27307603
DOI: 10.1093/nar/gkw539

[…] smc3 we used the crystal structure of smc3 (pdb id: 4ux3) as a template to create a model of smc3-l217p in i-tasser server (,). we analyzed the molecular dynamics of smc3 and smc3-l217p by using the elnemo server (). we examined the <r2> factor of both proteins, which represents their flexibility (supplementary figure s7). low <r2> indicates rigidity, while a high <r2> value […]

2014
PMCID: 4081090
PMID: 24920828
DOI: 10.1093/nar/gku486

[…] software inc.)., the crystal structure coordinate of milb was used for the normal mode analysis conducted using the web server developed by k. suhre and y.h. sanejouand (http://www.igs.cnrs-mrs.fr/elnemo/start.html). files of the 7th normal mode (i.e. the first vibrational mode with the lowest vibrational frequency, which is the most major vibrational mode of the system under investigation) […]


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ElNemo in publications

 (32)
PMCID: 5904202
PMID: 29696015
DOI: 10.3389/fimmu.2018.00674

[…] amplitudes of motion in representative structures of the unbound tcrs solved here were simulated using a combination of rigidity analysis and coarse-grained elastic network normal mode analysis. elnemo software () was used to obtain normal mode eigenvectors from coarse-grained elastic network modeling. first/froda software (, ) was used to carry out rigidity analysis (first) (), […]

PMCID: 5808480
PMID: 29431095
DOI: 10.1186/s12900-018-0080-9

[…] 12 software suite [] in order to avoid physically inaccessible torsion angles, bond lengths, and other structural properties., the wt and 35 mutant structures were modelled with en modelling using elnemo with the default parameters set []. the number of lowest frequency normal modes to be computed (nmodes) was set to 5. minimum, maximum perturbation parameters (dqmin/dqmax) and step size […]

PMCID: 5601205
PMID: 28677344
DOI: 10.1111/febs.14157

[…] of cwp2, cwp8 and lmw slp were prepared for flexibility analysis using pymol (www.pymol.org) and molprobity. normal mode eigenvectors were determined for the structures of the proteins using elnemo while first and froda were used to determine flexibility of the proteins. ten nontrivial modes were analysed and inspected with pymol to identify modes of motion that resulted in greater […]

PMCID: 5187391
PMID: 28066558
DOI: 10.1038/celldisc.2016.51

[…] analysis was performed as described before [, ]. briefly, the structural coordinates of castor1 were submitted for the nm analysis using the elastic network model server (http://www.igs.cnrsmrs.fr/elnemo/) [], which is a fast and simple tool to compute the major (that is, low-frequency) nms of a protein. the first vibrational mode (that is, the seventh nm, the first six modes […]

PMCID: 5187361
PMID: 28083537
DOI: 10.3389/fmolb.2016.00085

[…] and sanejouand, ; zheng and doniach, ; mahajan and sanejouand, )., during the past few years, several web-servers performing on-line normal mode analysis (nma) have been set up and described: elnemo (suhre and sanejouand, ), encom (frappier et al., ), [email protected] (tiwari et al., ), anm 2.0 (eyal et al., ), ad-enm (zheng and doniach, ), nmsim (kruger et al., ). we have extended and updated […]


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ElNemo institution(s)
Information Génomique & Structurale (UPR CNRS 2589), Marseille, France; Laboratoire de Physique, Ecole Normale Supérieure, Lyon, France

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