RosettaDock protocols

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RosettaDock statistics

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Associated diseases

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RosettaDock specifications

Information


Unique identifier OMICS_03779
Name RosettaDock
Interface Web user interface
Restrictions to use None
Operating system Other
Computer skills Basic
Stability Stable
Maintained Yes

Subtools


  • ACS (Adaptive Conformer Selection)
  • MDS (Motif Dock Score)

Maintainer


  • person_outline Jeffrey Gray <>

Publications for RosettaDock

RosettaDock in pipeline

2016
PMCID: 4860709
PMID: 27158082
DOI: 10.1038/srep25672

[…] the interaction of h-sn1 with tnfr1 (protein database [pdb] code: 1tnr) and analyze the binding regions. cabs-dock was first used to predict the initial complex structure of tnfr1 with h-sn1; rosettadock was employed for further flexible docking majorization. pymol software was chosen to visualize these structures., to evaluate the binding properties of h-sn1, affinity and competition […]


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RosettaDock in publications

 (93)
PMCID: 5955889
PMID: 29650980
DOI: 10.1038/s41598-018-23982-3

[…] of protein-dna recognition. we extracted the landscape features via principal component analysis (pca) using two distinct energy functions, one derived from piper sampling and the other using rosettadock. in both cases, we found that most of the variability (more than 75%) in the cluster can be explained by 3 (and sometimes 2) eigenvectors, suggesting that the energy landscape consists […]

PMCID: 5897410
PMID: 29651044
DOI: 10.1038/s41598-018-24068-w

[…] among the top 20 interaction models generated by patchdock,, the first and third model positioned the c terminal (last 12 residues) helix at the interface. these models were further refined with the rosettadock local refinement algorithm to generate models with atomistic detail of the interaction (fig. ). our top-ranking model positions aconitase in the reported substrate binding site […]

PMCID: 5751226
PMID: 29206185
DOI: 10.3390/ijms18122623

[…] of different methods utilized in homology modelling and docking follows, the methods have been chosen to be representative of some common successful methods as well as some less common approaches., rosettadock is a soft body type of protein interaction prediction software and considers backbone or side-chain flexibility, which is advantageous regarding obtaining structures of protein complexes […]

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

[…] monomer structures in docking, 35% (6/17) when using unbound, and 12% (2/17) when using the homology-modeled backbones to generate the complexes. increasing rigid-body diversity of the models using rosettadock’s local dock routine lowers the discrimination accuracy with the cognate antibody–antigen pair ranking in bound and unbound models but recovers additional top-ranked cognate complexes […]

PMCID: 5507604
PMID: 28662181
DOI: 10.1371/journal.ppat.1006448

[…] interactions with hl (denoted by the arrow in ). to obtain a more plausible model of the nm-acpi:hl complex, 10,000 independent docking simulations between rnm-acpi and hl were carried using rosettadock []. the resulting model () gave a complex in which the hl molecule was significantly further away from acp than from ba-plic, although this could be affected by loop flexibility […]


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RosettaDock institution(s)
Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA; Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD, USA; Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD, USA; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA; Department of Biochemistry, Institute for Protein Design University of Washington, Seattle, WA, USA
RosettaDock funding source(s)
Supported by the National Institutes of Health, USA (grant R01-GM078221).

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