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PyRosetta specifications


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 citations


In Depth Analysis of Human Neonatal and Adult IgM Antibody Repertoires

Front Immunol
PMCID: 5807330
PMID: 29459861
DOI: 10.3389/fimmu.2018.00128

[…] omatic 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, paving […]


A computational approach for designing D proteins with non canonical amino acid optimised binding affinity

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

[…] 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 fu […]


Computational design of a symmetrical β trefoil lectin with cancer cell binding activity

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

[…] kbone 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 did […]


Essential multimeric enzymes in kinetoplastid parasites: A host of potentially druggable protein protein interactions

PLoS Negl Trop Dis
PMCID: 5507555
PMID: 28662026
DOI: 10.1371/journal.pntd.0005720
call_split See protocol

[…] % similarity were excluded. The PDB files were cleaned to remove headers, retaining only ATOM line entries, using a shell script. Computational alanine scanning [] was performed using Rosetta 3.6 and PyRosetta [], with a modified version of the alanine-scanning script originally developed by the Gray lab []. The updated Talaris2013 scorefunction [] was parameterized to match an established general […]


Resurrecting the Dead (Molecules)

Comput Struct Biotechnol J
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 was produ […]


Impact of mutations in Toll like receptor pathway genes on esophageal carcinogenesis

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

[…] ntity (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 chain), […]

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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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