PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta

By Sidhartha Chaudhury, Sergey Lyskov, Jeffrey J. Gray. 2010

Subfields: Computational Biology & Bioinformatics, Computational Chemistry & Drug Discovery

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Citations in the corpus

Accurate prediction of protein structures and interactions using a 3-track neural network (2021, positive): “In the first, the predicted residue-residue distance and orientation distributions are fed into pyRosetta (5) to generate all-atom models.”
CopulaNet: Learning residue co-evolution directly from multiple sequence alignment for protein structure prediction (2020, positive): “Then, we use MinMover in PyRosetta[28] to search for the tertiary structure with the minimal potential, yielding (centroid) models.”
Rosetta3: An Object-Oriented Software Suite for the Simulation and Design of Macromolecules (2011, positive): “…new sequence for an RNA molecule (Das et al. , 2010) that would have been virtually impossible in ROSETTA 2, including Python bindings for all ROSETTA classes (Chaudhury et al. , 2010) and an interactive game, FOLDIT , which challenges users to predict a protein’s structure (Cooper et al. , 2010).”
RosettaAntibodyDesign (RAbD): A general framework for computational antibody design (2017, unknown): “This is an optional alternative for the minimization step One further option is in the inner loop is integrated sampling of the antibody-antigen orientation during design uses the underlying framework and docking algorithms of Rosetta-Dock [45,103–106].”
AdaLead: A simple and robust adaptive greedy search algorithm for sequence design (2020, unknown): “In this case we use PyRosetta (Chaudhury et al., 2010) as φ .”
Essentials of de novo protein design: Methods and applications (2018, unknown): “We illustrate many aspects of this review in the view of using Rosetta (i.e., Rosetta/Rosetta-Scripts/PyRosetta) 15 – 17 as the prime protein design software, but the concepts are general enough that it should be possible to translate them to other available molecular-modeling suites.”
Integrative protein modeling in RosettaNMR from sparse paramagnetic restraints (2019, unknown): “Rosetta allows manipulating the protein through modeling objects accessible from high-level scripting languages such as PyRosetta (Chaudhury et al., 2010) and Rosetta Scripts (Fleishman et al., 2011).”
Protein sequence optimization with a pairwise decomposable penalty for buried unsatisfied hydrogen bonds (2020, unknown): “3Å probe size and were generated using PyRosetta[7].”
Protein sequence design with a learned potential (2020, unknown): “We use PyRosetta implementations of these metrics and monitor them over the course of sampling [87].”
OpenStructure: an integrated software framework for computational structural biology (2013, unknown): “…are many bio-informatics and structural biology toolkits that are either completely implemented in Python or provide a well maintained Python wrapper to their functionality (Sukumaran & Holder, 2010; Chaudhury et al. , 2010; Hinsen & Sadron, 2000; Kohlbacher & Lenhof, 2000; Adams et al. , 2011).”