PyRosetta specifications

Information


Unique identifier OMICS_05477
Name PyRosetta
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for PyRosetta

PyRosetta in publications

 (30)
PMCID: 5807330
PMID: 29459861
DOI: 10.3389/fimmu.2018.00128

[…] mutations throughout the entire antibody heavy chain. moreover, the structural analysis of antigen-antibody complexes in repertoire-scale could be facilitated by bioinformatics methods such as pyrosetta or rosetta antibody (). these information may guide the design of vaccine candidates able to induce antibodies encoded by the most frequently used vdj rearrangements in an individual, […]

PMCID: 5673230
PMID: 29108013
DOI: 10.1371/journal.pone.0187524

[…] together with the original crystal structure, were used as the models for mutation calculations using rosetta., rosetta modelling calculations were carried out using the python based interface: pyrosetta[]. the native vegf-d-rfx001 complex pdb file was first reformatted for compatibility with rosetta, followed by calculation of the native rosetta energy score using the ‘full atom’ scoring […]

PMCID: 5517649
PMID: 28724971
DOI: 10.1038/s41598-017-06332-7

[…] energy minimised using moe (molecular operating environment, chemical computing group, montreal, canada). the predicted ancestral sequences were mapped onto the symmetrised backbone model using pyrosetta, , and each sequence was ranked by the rosetta score. with only three related basis sequences to work with, only a limited region of sequence space could be sampled and the model scores […]

PMCID: 5472138
PMID: 28652896
DOI: 10.1016/j.csbj.2017.05.002

[…] original ancestral protein. this blade was used to model a perfectly 6-fold symmetrical propeller protein using rosettadock and potential ancestor sequences were modelled onto this scaffold using a pyrosetta based procedure and the lowest energy structures were identified . molecular biology techniques were used to synthesize the gene encoding pizza protein and the recombinant protein […]

PMCID: 5460900
PMID: 28531216
DOI: 10.1371/journal.pgen.1006808

[…] (61% similarity with blosum50 matrix) over the 143 residues of the tlr4 tir domain. tlr4 ectodomain model energy minimization, was with foldx 3.0 [], and tir dimer contacts were optimized using pyrosetta []. contacting tlr4 residues less than 0.5 å apart at surfaces were determined using ucsf chimera and sorted by residue range in mathematica(tm) to show dimer contacts (to other tlr4 […]


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PyRosetta institution(s)
Program in Molecular Biophysics, Sidney Kimmel Comprehensive Cancer Center and Institute of Computational Medicine, Johns Hopkins University, Baltimore, MD, USA

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