NOMAD-Ref protocols

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NOMAD-Ref specifications


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 in pipelines

PMCID: 5099264
PMID: 27843768
DOI: 10.1016/j.gdata.2016.10.009

[…] regions. the corresponding position was performed utilizing swiss-port considered separately to receive altered protein model structures. the energy minimizations accomplished by yasara and nomad-ref gromacs using force field energy for the native type protein pkhd1 protein structure and mutant type protein structure based on the protein model rmsd. the complete energy of native […]

PMCID: 3173608
PMID: 21893289
DOI: 10.1016/j.str.2011.05.015

[…] cluster analysis, and secondary structure predictions (). the tm helix was modeled by mutating the equivalent region in wza using coot () followed by energy minimization by gromacs using the nomad-ref server ( phyre was used to identify homologs of csgg16-226 and create the homology models of the periplasmic domain based on structures of tolb and duf330 […]

PMCID: 3197589
PMID: 22028795
DOI: 10.1371/journal.pone.0025876

[…] (e→v). the mutations for 4hhb at the corresponding positions were achieved using swiss-port viewed separately to obtain altered model structures. the energy minimizations were achieved by yasara and nomad-ref gromacs server using force field energy for the native type protein 4hhb and mutant type protein structures from the protein model rmsd. the total energy of native structure 4hhb and mutant […]

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NOMAD-Ref in publications

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 ( []. conjugate gradient method was used for energy minimization of the 3d structures., project have your protein explained (hope; […]

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) […]

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 ( the nomad-ref server utilizes gromacs using conjugant gradient force fields for energy minimization […]

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 […]

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 […]

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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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