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Protocols

NOMAD-Ref specifications

Information


Unique identifier OMICS_07559
Name NOMAD-Ref
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for NOMAD-Ref

NOMAD-Ref citations

 (35)
library_books

Phenotype prediction for mucopolysaccharidosis type I by in silico analysis

2017
PMCID: 5496269
PMID: 28676128
DOI: 10.1186/s13023-017-0678-1

[…] used for detection of a stretch of similar residues at sequence level to obtain a structural fit between the two models. energy minimization for three-dimensional (3d) structures was performed using nomad-ref server (http://lorentz.immstr.pasteur.fr/nomad-ref.php) []. conjugate gradient method was used for energy minimization of the 3d structures., project have your protein explained (hope; […]

library_books

Whole exome sequencing of a consanguineous family identifies the possible modifying effect of a globally rare AK5 allelic variant in celiac disease development among Saudi patients

2017
PMCID: 5432167
PMID: 28505210
DOI: 10.1371/journal.pone.0176664

[…] as template (pdbid: 2bwj) for creating mutant protein versions through homology modeling. then, the energy minimization step for full-length wild-type and mutant protein structures was done using nomad-ref server []. in next stages, the amino acid substitution induced structural disturbances in ak5 protein molecule was measured through a computational (cα traces and backbone atoms) […]

library_books

Computational Modeling of complete HOXB13 protein for predicting the functional effect of SNPs and the associated role in hereditary prostate cancer

2017
PMCID: 5363706
PMID: 28272408
DOI: 10.1038/srep43830

[…] taken as the native protein., each mutant model (21 models) was generated using the “mutation” tool in swisspdbviewer. energy minimization of the native and the mutated protein was carried out using nomad-ref gromacs server (http://lorentz.immstr.pasteur.fr/gromacs/minimization_submission.php). the nomad-ref server utilizes gromacs using conjugant gradient force fields for energy minimization […]

library_books

Rational design of DKK3 structure based small peptides as antagonists of Wnt signaling pathway and in silico evaluation of their efficiency

2017
PMCID: 5325476
PMID: 28234935
DOI: 10.1371/journal.pone.0172217

[…] of wnt signaling pathway. modeller 9.15 package was used to predict 3d structure of crd2 based on the homology modeling (hm) protocol. after refinement and minimization with galaxyrefine and nomad-ref servers, the quality of selected models was evaluated utilizing vadar, saves and prosa servers. molecular docking studies as well as literature-based information revealed two distinct boxes […]

library_books

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

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

[…] 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 own server, nomad-ref (lindahl et al., ), with a new and user-friendlier interface, including a better visual representation of the results while at the same time enlarging the performances of the core […]

library_books

Leptospira surface adhesin (Lsa21) induces Toll like receptor 2 and 4 mediated inflammatory responses in macrophages

2016
PMCID: 5172228
PMID: 27996041
DOI: 10.1038/srep39530

[…] which generated five top best predicted structures with high c-score. a structure in agreement with ramachandran plot was selected for further energy minimization using steepest descent algorithm in nomad-ref online program (http://lorentz.dynstr.pasteur.fr/docking/submission.php). the energy minimized structure was used to create a docking model on human tlr2 and tlr4 structure using zdock […]


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NOMAD-Ref institution(s)
Unite de Dynamique Structurale des Macromolécules, URA 2185 du CNRS, Institut Pasteur Paris, France

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