Rosetta software suite statistics

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Rosetta software suite specifications

Information


Unique identifier OMICS_04468
Name Rosetta software suite
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux
Computer skills Advanced
Version 3.9
Stability Stable
Maintained Yes

Subtools


  • AbDesign
  • DRRAFTER
  • FunFolDes
  • ProteinLigEnsemble
  • RAbD (RosettaAntibodyDesign)
  • RosettaHoles
  • RosettaLigand
  • RosettaLigandEnsemble
  • RosettaSurface

Versioning


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Maintainer


  • person_outline David Baker <>

Additional information


https://www.rosettacommons.org/docs/latest/Home

Publications for Rosetta software suite

Rosetta software suite in publications

 (54)
PMCID: 5944921
PMID: 29746590
DOI: 10.1371/journal.ppat.1006986

[…] coot []. a library of 200 homologous 7-mer peptide fragment coordinates per relevant residue were compiled and used in iterative centroid-representation density-guided rebuild-and-refinement in the rosetta software suite []. rosetta models were manually adjusted in coot followed by evaluation based on geometry (molprobity []) and cryo-em density fit (emringer []). upon convergence, the best […]

PMCID: 5930395
PMID: 29725615
DOI: 10.1126/sciadv.aar3219

[…] into calcite, can be largely attributed to its strong binding to mineral occurring through the acidic peptide stretches in its primary amino acid sequence (). we thus computationally modeled, using rosettasurface (), docking of the highly acidic polyaspartate sequence found in chicken opn (99dddddddnd107) to acute and obtuse growth steps of calcite (). the binding energies to these two calcite […]

PMCID: 5849751
PMID: 29535329
DOI: 10.1038/s41598-018-22476-6

[…] at the upper limit of what is currently achieved with other, specifically trained methods. our implicit potentials can be used to improve energy functions in computational modeling tools such as the rosetta software suite,,, or md simulation approaches–, especially accounting for asymmetry that is inherent in membrane bilayers. possible applications of these potentials are manifold, […]

PMCID: 5833279
PMID: 29451898
DOI: 10.1371/journal.pcbi.1005999

[…] and as a result current design methods only sample a fraction of available sequence space. we propose a new computational approach that combines traditional structure-based modeling using the rosetta software suite with machine learning and integer linear programming to overcome limitations in the rosetta sampling methods. we demonstrate the effectiveness of this method, which we call […]

PMCID: 5797543
PMID: 29441070
DOI: 10.3389/fimmu.2018.00099

[…] considered manually, and the rotamer giving the lowest strain was used in our final structural model in figure s6a in supplementary material. peptide/mhc-binding energies were computed using the rosetta software suite. average binding energies of residue-specific interactions were calculated using the residue_energy_breakdown protocol in rosetta., to assess the ability of our alk neoepitopes […]


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Rosetta software suite institution(s)
Biophysics Program, Stanford University, Stanford, CA, USA; Electron Imaging Center for Nanomachines University of California, Los Angeles (UCLA), Los Angeles, CA, USA; Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA, USA; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA; Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA; Department of Biochemistry and Molecular Genetics, University of Colorado Denver Anschutz Medical Campus, Aurora, CO, USA; Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA; Department of Physics, Stanford University, Stanford, CA, USA
Rosetta software suite funding source(s)
Supported by NIH Shared Instrumentation Grant 1S10RR02664701, a Gabilan Stanford Graduate Fellowship, a NSF GRFP, T32- GM008294 (Molecular Biophysics Training Program), NIGMS MIRA R35 GM122579, R01 GM121487, and NIH grant GM114178.

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