Robetta protocols

View Robetta computational protocol

Robetta statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.

Subscribe
info

Citations per year

Citations chart
info

Popular tool citations

chevron_left Tertiary structure prediction Hot spot prediction chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

Robetta specifications

Information


Unique identifier OMICS_03868
Name Robetta
Interface Web user interface
Restrictions to use Academic or non-commercial use
Computer skills Basic
Stability Beta
Maintained Yes

Maintainer


  • person_outline David Baker <>

Publication for Robetta

Robetta in pipelines

 (14)
2017
PMCID: 5378476
PMID: 28300532
DOI: 10.7554/eLife.23687.026

[…] was modeled de novo in coot (rrid:scr_014222) (), using an initial structure predicted by robetta (). the secondary structure in our resulting model of afra is consistent with those predicted by robetta and i-tasser (rrid:scr_014627) (). initial protein and ribosome domain fitting into cryo-em maps was performed using chimera (rrid:scr_004097) (), followed by manual modeling using pymol […]

2017
PMCID: 5405553
PMID: 28446174
DOI: 10.1186/s12918-017-0427-z

[…] the nucleotide of interest was at a position for easy read during sanger sequencing. amplification and sequencing was performed by eurofins genomics india pvt. ltd., ab-initio models were made using robetta server [] (http://robetta.bakerlab.org) except for rpsl (homology modeling was used) and the models generated were checked for various parameters for model assessment, such as ramachandran […]

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

[…] 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 []. mutations were performed with ucsf chimera [] […]

2017
PMCID: 5622079
PMID: 28963468
DOI: 10.1038/s41467-017-00785-0

[…] then replaced by the crystal structure of human lrs cp1 domain (pdb 2wfda) by superimposition using the pairwise dalilite server. the model prediction of the c-terminal une-l domain was performed by robetta online rosetta server using chain a of linear ubiquitin and antibody fab fragment complex crystal structure as template (pdb 3u30a). the structural model prediction for the cd, abd, and vc […]

2017
PMCID: 5660449
PMID: 29078764
DOI: 10.1186/s12915-017-0438-7

[…] and analyzed an ensemble of optimized loop structures using the loopmodel module of rosetta 2016.46.59086 []. fragment libraries were generated for the full-length protein of each target using the robetta web server [], and thousands of loop models (2000 for s. enterica flge and 3500 for c . jejuni flge) were subsequently obtained using the quick_ccd modeling method and refine_ccd refinement […]


To access a full list of citations, you will need to upgrade to our premium service.

Robetta in publications

 (214)
PMCID: 5950140
PMID: 29759072
DOI: 10.1186/s12929-018-0444-2

[…] ratio, ci confidence interval, the n-terminal domains (1st-126th residue) of the m isoform of chat non-mutant protein and mutant a120t of the same isoform were prepared using ab initio modelling robetta server (http://robetta.bakerlab.org/) and homology modelling software modeller []. search for hydrogen bond network was done via vmd [], schrodinger maestro software (schrodinger, l. […]

PMCID: 5936065
PMID: 29618456
DOI: 10.1242/bio.033977

[…] that we consulted include raptorx at http://raptorx.uchicago.edu/structureprediction/ () (a); metadisorder at http://genesilico.pl/metadisorder/ (); phyre2 at http://www.sbg.bio.ic.ac.uk/~phyre2 (); robetta at http://robetta.bakerlab.org (); and the eukaryotic linear motif resource at http://elm.eu.org (). each of these sites similarly predicted that regions with well-defined tertiary structure […]

PMCID: 5832097
PMID: 29666707
DOI: 10.1155/2018/5659683

[…] as found in this lipase molecule []. recently, amino acid sequence of lipase from s. arlettae jpbw-1 was characterized using maldi-tof-ms analysis and comparative modelling approach was performed via robetta server to postulate a structure-activity relationship of the lipase []. in one study, it was found that ta lipase from cohnella sp. a01 was structurally determined to be 37.5%  α-helix, 12.8%  […]

PMCID: 5764122
PMID: 29126780
DOI: 10.1016/j.bbabio.2017.11.001

[…] helices (tmhs). hydrophobicity profiles were performed using the protscale/transmembrane tendency application in www.expasy.org . structural models of rpa4402 were generated using the quark and robetta servers., photosynthetic membranes were isolated from wt rps. palustris cells by rate zonal centrifugation. rc-lh1 core complexes were then purified after a further rate zonal centrifugation […]

PMCID: 5781290
PMID: 29361909
DOI: 10.1186/s12859-018-2010-z

[…] derived homology model. to begin, we applied nine computational modeling algorithms to the protein sequence: genesilico [], hhpred [], i-tasser [], m4t [], pcons5 [], phyre2 [], raptorx [], robetta [], and swiss-model []. raptorx produced the highest-coverage model, which consisted of two well-folded domains spanning residues 1–769 and 881–1151. this model was based on seven pdb […]


To access a full list of publications, you will need to upgrade to our premium service.

Robetta institution(s)
Structural Genomics of Pathogenic Protozoa, Department of Biochemistry, University of Washington, Seattle WA, USA
Robetta funding source(s)
Supported by NIH grant No. P50 GM64655 and the Howard Hughes Medical Institute.

Robetta reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review Robetta