RaptorX protocols

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RaptorX specifications

Information


Unique identifier OMICS_03746
Name RaptorX
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Subtool


  • DeepThreader

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Information


Unique identifier OMICS_03746
Name RaptorX
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Subtool


  • DeepThreader

Publications for RaptorX

RaptorX in pipelines

 (9)
2018
PMCID: 5862659
PMID: 29198957
DOI: 10.1016/j.jmb.2017.11.014

[…] profiles were used to search against profile databases with hhsearch ., protein structures were modeled by submitting corresponding protein sequences to automatic homology modeling servers, raptorx and i-tasser . two different servers were used to ensure the reliability of obtained models following the observation that, if models generated by different methods are similar, these models […]

2017
PMCID: 5435356
PMID: 28475612
DOI: 10.1371/journal.ppat.1006379

[…] described []., comparative models were built from template x-ray crystal structures from the protein database (pdb) files that were identified by searching and aligned using hhsearch/hhpred [], raptorx [], and sparks-x [] as implemented on the robetta server (robetta.org<http://robetta.org>). alignments were clustered and comparative models were generated using the rosettacm protocol […]

2016
PMCID: 4909266
PMID: 27304881
DOI: 10.1371/journal.pone.0156838

[…] conserved domains. brevibacillus phage conserved domains were compared to the c2 repressor of salmonella phage p22 (s. enterica serovar typhimurium) [1adr_a, 2r1j_l, 3jxb_c] []. hhpred [] and raptorx [–] were used to predict tertiary structure and binding sites. these predicted structures were then superimposed using strap [] and compared using ncbi’s cn3d []., phamerator [] was used […]

2016
PMCID: 4973958
PMID: 27489951
DOI: 10.1371/journal.pone.0160544

[…] germany). the images were captured using chemidoc xrs equipment (bio-rad, münchen, germany)., to access the location of the identified epitope of mab-3f8, the structure of fba was predicted using raptorx online software [] using standard settings. coth online software was used to calculate the dimer interfaces for fba []. all structure manipulation and image acquirement were done with pymol […]

2015
PMCID: 4451034
PMID: 26038731
DOI: 10.7717/peerj.976

[…] variation., given the support for diversifying selection it is worthwhile to ask if predictions of protein structure of the active peptide would add support for the role of selection. we used the raptorx protein structure server (http://raptorx.uchicago.edu/, ) to predict secondary structure of exon 4, the active peptide. this program can give some predictions of structure without the use […]


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RaptorX in publications

 (164)
PMCID: 5943604
PMID: 29743632
DOI: 10.1038/s41598-018-25667-3

[…] in identification of a particularly well-conserved region (exon 4 to exon 5) within the ocia domain (fig. ). interestingly, in silico analysis using various structure prediction programs such as raptorx (raptorx.uchicago.edu/) and phyre (http://www.sbg.bio.ic.ac.uk/~phyre2/html/page.cgi?id=index) showed that the region ranging from exon 3 to exon 6 is indeed an important part of the ociad1/2 […]

PMCID: 5915450
PMID: 29691429
DOI: 10.1038/s41598-018-24344-9

[…] deleted that were more than 40 å away from the center of mass of ery. initial structures of ermcl (sequence: mgifsifvi) and h-ns (msealkilnnir) peptides off of the ribosome were created using the raptorx webserver and equilibrated in bulk solution using molecular dynamics (md) simulations. specifically, the peptides were solvated in a cubic box with tip3p water molecules […]

PMCID: 5897026
PMID: 29649335
DOI: 10.1371/journal.pone.0195783

[…] protein was modelled using phyre2 online server []. modelled protein structure was refined using modrefiner []. calcium ions binding sites were predicted using raptor x binding online server (http://raptorx.uchicago.edu/bindingsite/) or coach for protein-ligand binding site prediction (http://zhanglab.ccmb.med.umich.edu/coach/) []. various domains of lslpr protein was predicted using smart […]

PMCID: 5923482
PMID: 29642590
DOI: 10.3390/v10040188

[…] these predicted gene products have no similarity to any other toxins. finally, in some unique cases protein structure modeling can provide clarity. open-source computational modeling software, like raptorx [] and i-tasser [], can be used to predict the integrity of enzymes or identify functions based on similarity to known protein structures rather than sequence similarity in order to refine […]

PMCID: 5902962
PMID: 29692986
DOI: 10.3389/fchem.2018.00101

[…] strains and plasmids were obtained from merck kgaa. all chemicals used were obtained at highest purity from roth chemicals or applichem gmbh. enzymes were purchased from thermo fisher scientific., raptorx was applied for homology modeling studies (http://raptorx.uchicago.edu; källberg et al., ). the initial predicted structure was analyzed and further modified in the environment of ucsf […]


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RaptorX institution(s)
Toyota Technological Institute, Chicago, IL, USA

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