Real-Time PyMOL Visualization for Rosetta and PyRosetta
By E. Baugh, Sergey Lyskov, Brian D. Weitzner, Jeffrey J. Gray. 2011
89 citations recorded by the source corpus.
Computational structure prediction and design of proteins and protein-protein complexes have long been inaccessible to those not directly involved in the field. A key missing component has been the ability to visualize the progress of calculations to better understand them. Rosetta is one simulation suite that would benefit from a robust real-time visualization solution. Several tools exist for the sole purpose of visualizing biomolecules; one of the most popular tools, PyMOL (Schrödinger), is a powerful, highly extensible, user friendly, and attractive package. Integrating Rosetta and PyMOL directly has many technical and logistical obstacles inhibiting usage. To circumvent these issues, we developed a novel solution based on transmitting biomolecular structure and energy information via UDP sockets. Rosetta and PyMOL run as separate processes, thereby avoiding many technical obstacles while visualizing information on-demand in real-time. When Rosetta detects changes in the structure of a protein, new coordinates are sent over a UDP network socket to a PyMOL instance running a UDP socket listener. PyMOL then interprets and displays the molecule. This implementation also allows remote execution of Rosetta. When combined with PyRosetta, this visualization solution provides an interactive environment for protein structure prediction and design.
Subfields: Information Systems and Management, Molecular Biology
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In Information Systems and Management
In Molecular Biology
- Jeffrey J. Gray
- Brian D. Weitzner
- Sidhartha Chaudhury
- Monica Berrondo
- Pravin Muthu
- Hannah Bergman
- Shuguang Yuan
- H. C. Stephen Chan
Citations in the corpus
- Benchmarking and Analysis of Protein Docking Performance in Rosetta v3.2 (2011, methodology): “Finally, user interfaces such as RosettaScripts,[22] PyRosetta [23], and a PyMol interface [24] were developed to provide unprecedented accessibility of the code.”
- An Integrated Framework Advancing Membrane Protein Modeling and Design (2015, unknown): “Rosetta’s PyMOLMover transmits coordinate information from the Pose in Rosetta to PyMOL in real time [44].”
- Using PyMOL as a platform for computational drug design (2017, methodology): “33,34”