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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

Versioning


No version available

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 citations

 (186)
library_books

A double helical motif in OCIAD2 is essential for its localization, interactions and STAT3 activation

2018
Sci Rep
PMCID: 5943604
PMID: 29743632
DOI: 10.1038/s41598-018-25667-3

[…] zed to compare the transcript-expression levels of ociad1 and ociad2. For predicting structure of zebrafish, mouse, and human OCIAD1 and OCIAD2 proteins, various structure prediction programs such as RaptorX (http://raptorx.uchicago.edu/) and Phyre (http://www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi?id=index) were used wherein the amino acid sequences of these proteins corresponding to Uniprot IDs Q […]

library_books

Investigation of immunogenic properties of Hemolin from silkworm, Bombyx mori as carrier protein: an immunoinformatic approach

2018
Sci Rep
PMCID: 5934409
PMID: 29725106
DOI: 10.1038/s41598-018-25374-z

[…] hp?id=779) and it determines the percentage of helix, stands and coils. An average Q3 score of PSIPRED 3.2 server is 81.6%. The tertiary structure of hemolin protein was predicted by web based server RaptorX (http://raptorx.uchicago.edu/StructurePrediction/predict/) based on template available.RaptorX generates high-quality tertiary structure models by multiple templates, the confidence score of t […]

call_split

Erythromycin leads to differential protein expression through differences in electrostatic and dispersion interactions with nascent proteins

2018
Sci Rep
PMCID: 5915450
PMID: 29691429
DOI: 10.1038/s41598-018-24344-9
call_split See protocol

[…] ere 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 and the AMBER99SB-ILDN […]

library_books

Molecular characterization of the lipophorin receptor in the crustacean ectoparasite Lepeophtheirus salmonis

2018
PLoS One
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 (http: […]

library_books

Characterizing Phage Genomes for Therapeutic Applications

2018
Viruses
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 the […]

library_books

Insights Into the Bifunctional Aphidicolan 16 ß ol Synthase Through Rapid Biomolecular Modeling Approaches

2018
PMCID: 5902962
PMID: 29692986
DOI: 10.3389/fchem.2018.00101

[…] 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 Chimera […]

Citations

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

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