Rosetta software suite statistics

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Citations per year

Number of citations per year for the bioinformatics software tool Rosetta software suite
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Tool usage distribution map

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Associated diseases

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Popular tool citations

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Protocols

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


No version available

Maintainer


  • person_outline David Baker

Additional information


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

Publications for Rosetta software suite

Rosetta software suite citations

 (72)
call_split

Structural and immunologic correlates of chemically stabilized HIV 1 envelope glycoproteins

2018
PLoS Pathog
PMCID: 5944921
PMID: 29746590
DOI: 10.1371/journal.ppat.1006986
call_split See protocol

[…] d 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 mode […]

library_books

RosettaLigandEnsemble: A Small Molecule Ensemble Driven Docking Approach

2018
PMCID: 5928483
PMID: 29732444
DOI: 10.1021/acsomega.7b02059

[…] RosettaLigand,, a small docking tool within the Rosetta structural biology modeling software suite, is one of several algorithms developed for this purpose in the last few decades. AutoDock, DOCK, and […]

library_books

Nanostructure, osteopontin, and mechanical properties of calcitic avian eggshell

2018
Sci Adv
PMCID: 5930395
PMID: 29725615
DOI: 10.1126/sciadv.aar3219

[…] n 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 s […]

library_books

Statistically derived asymmetric membrane potentials from α helical and β barrel membrane proteins

2018
Sci Rep
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, and we have s […]

library_books

Development of Erasin: a chromone based STAT3 inhibitor which induces apoptosis in Erlotinib resistant lung cancer cells

2017
Sci Rep
PMCID: 5727211
PMID: 29234062
DOI: 10.1038/s41598-017-17600-x

[…] ificant activity against the more distantly related SH2 domain of the tyrosine kinase Lck (Supplementary Table ).Figure 2 Flexible docking of compounds 1, 4, 6, 7, and 8 to the STAT3 SH2 domain using RosettaLigand identified four clusters of highly populated binding poses for all five docked compounds (Supplementary Fig. ). The binding poses in cluster 3 show a binding pocket for substituents at t […]

library_books

A cyber linked undergraduate research experience in computational biomolecular structure prediction and design

2017
PLoS Comput Biol
PMCID: 5720517
PMID: 29216185
DOI: 10.1371/journal.pcbi.1005837

[…] unique needs and challenges of computational biology.We created a new REU program within the Rosetta Commons, a group formed to enable close collaboration between 52 (and growing) labs developing the Rosetta software suite for biomolecular structure prediction and design. The Rosetta Commons labs are united by a set of core challenges, including (1) sampling macromolecular conformational space, (2 […]


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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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