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Protocols

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 citations

 (36)
library_books

In Silico and Structural Analyses Demonstrate That Intrinsic Protein Motions Guide T Cell Receptor Complementarity Determining Region Loop Flexibility

2018
Front Immunol
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) (), which identif […]

library_books

Molecular mechanisms underlying the impact of mutations in SOD1 on its conformational properties associated with amyotrophic lateral sclerosis as revealed with molecular modelling

2018
BMC Struct Biol
PMCID: 5808480
PMID: 29431095
DOI: 10.1186/s12900-018-0080-9

[…] MBER 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 betwee […]

library_books

RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview

2018
PMCID: 5920944
PMID: 29297679
DOI: 10.1021/acs.chemrev.7b00427

[…] al., who studied three three-way junctions extracted from the large ribosomal subunits using all-atom MD and compared the results obtained to data from ENM calculations and a block analysis using the ElNemo software package. They found that for the GTPase associated center part of 23S rRNA ENM failed to predict the hinge region observed by all-atom MD at the three-way junction. Further, the all-at […]

call_split

Cwp2 from Clostridium difficile exhibits an extended three domain fold and cell adhesion in vitro

2017
PMCID: 5601205
PMID: 28677344
DOI: 10.1111/febs.14157
call_split See protocol

[…] ctures 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 sim […]

call_split

Arabidopsis thaliana dehydroascorbate reductase 2: Conformational flexibility during catalysis

2017
Sci Rep
PMCID: 5307357
PMID: 28195196
DOI: 10.1038/srep42494
call_split See protocol

[…] h the DynDom web server (http://fizz.cmp.uea.ac.uk/dyndom/). Secondary structure elements were assigned with Stride (http://webclu.bio.wzw.tum.de/stride/). Normal mode analysis was carried out in the elNémo (http://igs-server.cnrs-mrs.fr/elnemo/index.html) and ANM 2.0 (http://anm.csb.pitt.edu) web servers with default parameters. Structural superposition was performed in the Superpose module of CC […]

library_books

Comparative Normal Mode Analysis of the Dynamics of DENV and ZIKV Capsids

2016
Front Mol Biosci
PMCID: 5187361
PMID: 28083537
DOI: 10.3389/fmolb.2016.00085

[…] ; Delarue 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 our o […]


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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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