Real-Time PyMOL Visualization for Rosetta and PyRosetta
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...
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| Format: | Online |
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Public Library of Science
2011
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| Online Access: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3156697/ |
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pubmed-3156697 |
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oai_dc |
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pubmed-31566972011-08-19 Real-Time PyMOL Visualization for Rosetta and PyRosetta Baugh, Evan H. Lyskov, Sergey Weitzner, Brian D. Gray, Jeffrey J. Research Article 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. Public Library of Science 2011-08-16 /pmc/articles/PMC3156697/ /pubmed/21857909 http://dx.doi.org/10.1371/journal.pone.0021931 Text en Baugh et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited. |
| repository_type |
Open Access Journal |
| institution_category |
Foreign Institution |
| institution |
US National Center for Biotechnology Information |
| building |
NCBI PubMed |
| collection |
Online Access |
| language |
English |
| format |
Online |
| author |
Baugh, Evan H. Lyskov, Sergey Weitzner, Brian D. Gray, Jeffrey J. |
| spellingShingle |
Baugh, Evan H. Lyskov, Sergey Weitzner, Brian D. Gray, Jeffrey J. Real-Time PyMOL Visualization for Rosetta and PyRosetta |
| author_facet |
Baugh, Evan H. Lyskov, Sergey Weitzner, Brian D. Gray, Jeffrey J. |
| author_sort |
Baugh, Evan H. |
| title |
Real-Time PyMOL Visualization for Rosetta and PyRosetta |
| title_short |
Real-Time PyMOL Visualization for Rosetta and PyRosetta |
| title_full |
Real-Time PyMOL Visualization for Rosetta and PyRosetta |
| title_fullStr |
Real-Time PyMOL Visualization for Rosetta and PyRosetta |
| title_full_unstemmed |
Real-Time PyMOL Visualization for Rosetta and PyRosetta |
| title_sort |
real-time pymol visualization for rosetta and pyrosetta |
| description |
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. |
| publisher |
Public Library of Science |
| publishDate |
2011 |
| url |
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3156697/ |
| _version_ |
1611471011447832576 |