RosettaAntibody protocols

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RosettaAntibody specifications

Information


Unique identifier OMICS_08690
Name RosettaAntibody
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publications for RosettaAntibody

RosettaAntibody in pipeline

2017
PMCID: 5312500
PMID: 28228926
DOI: 10.1016/j.csbj.2017.01.010

[…] fread has been shown to produce sub-ångström predictions for the five canonical cdrs (0.81  å, 0.42  å, 0.96  å, 0.98 å and 0.88  å for l1–h2), while the average accuracy for h3 loops is 2.25  å . rosettaantibody also produces sub-ångström predictions for the other cdr loops (0.78  å, 0.54  å, 0.81  å, 0.84  å and 0.93  å), while the accuracy of h3 prediction ranges between 1.6  å and 6.0  å […]


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RosettaAntibody in publications

 (16)
PMCID: 5857718
PMID: 29560474
DOI: 10.1016/j.heliyon.2018.e00564

[…] tandem can bind in the same way as whole protein gp350/220. lastly, the structure of anti-gp350 antibody was modeled using a homology modeling server for the antibody variable region of interest (rosettaantibody) according to mab 72a1 heavy- and light-chain variable region sequences ., prediction of protein stability of single and tandem epitopes was calculated using protparam software . […]

PMCID: 5840193
PMID: 29545810
DOI: 10.3389/fimmu.2018.00413

[…] rigidifies the cdr-h3 loop. thus, we hypothesize that this effect should be observable in a repertoire-scale study of thousands of antibodies. we first analyzed thousands of recently determined rosettaantibody homology models of the most common antibody sequences found in the human peripheral blood cell repertoire (). we estimated the structural flexibility of the cdr-h3 loop by applying […]

PMCID: 5727015
PMID: 29276518
DOI: 10.3389/fimmu.2017.01753

[…] methods create a large number of potential conformations, often referred to as decoys (), which makes them computationally expensive compared with homology methods. ab initio approaches include rosettaantibody () and plop (). rosettaantibody is accessible online via the rosie () website, where a quick antibody modeling option is available which omits the step of intensive searching […]

PMCID: 5579192
PMID: 28860479
DOI: 10.1038/s41598-017-10737-9

[…] two of which bound dykd with high specificity. second, grafting cdrs into frameworks can be structurally disruptive and/or require compensating changes to framework residues. notably, pigs and rosettaantibody predicted main chain breaks in select optcdr designs (data not shown), suggesting the structures may be poorly matched to the underlying framework. this interpretation is supported […]

PMCID: 5557897
PMID: 28811664
DOI: 10.1038/s41598-017-08414-y

[…] identification of the correct antibody–antigen interaction partners. we evaluate the effects of antibody backbone accuracy on the partner predictions using antibody bound, unbound structures, and rosettaantibody generated homology models. we also demonstrate the effects of increasing diversity of the generated cognate and non-cognate models on prediction accuracy. to our knowledge, our work […]


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RosettaAntibody institution(s)
Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA

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