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Fast and versatile sequence-independent protein docking for nanomaterials design using RPXDock

Computationally designed multi-subunit assemblies have shown considerable promise for a variety of applications, including a new generation of potent vaccines. One of the major routes to such materials is rigid body sequence-independent docking of cyclic oligomers into architectures with point group...

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Autores principales: Sheffler, William, Yang, Erin C., Dowling, Quinton, Hsia, Yang, Fries, Chelsea N., Stanislaw, Jenna, Langowski, Mark D., Brandys, Marisa, Li, Zhe, Skotheim, Rebecca, Borst, Andrew J., Khmelinskaia, Alena, King, Neil P., Baker, David
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10237659/
https://www.ncbi.nlm.nih.gov/pubmed/37216343
http://dx.doi.org/10.1371/journal.pcbi.1010680
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author Sheffler, William
Yang, Erin C.
Dowling, Quinton
Hsia, Yang
Fries, Chelsea N.
Stanislaw, Jenna
Langowski, Mark D.
Brandys, Marisa
Li, Zhe
Skotheim, Rebecca
Borst, Andrew J.
Khmelinskaia, Alena
King, Neil P.
Baker, David
author_facet Sheffler, William
Yang, Erin C.
Dowling, Quinton
Hsia, Yang
Fries, Chelsea N.
Stanislaw, Jenna
Langowski, Mark D.
Brandys, Marisa
Li, Zhe
Skotheim, Rebecca
Borst, Andrew J.
Khmelinskaia, Alena
King, Neil P.
Baker, David
author_sort Sheffler, William
collection PubMed
description Computationally designed multi-subunit assemblies have shown considerable promise for a variety of applications, including a new generation of potent vaccines. One of the major routes to such materials is rigid body sequence-independent docking of cyclic oligomers into architectures with point group or lattice symmetries. Current methods for docking and designing such assemblies are tailored to specific classes of symmetry and are difficult to modify for novel applications. Here we describe RPXDock, a fast, flexible, and modular software package for sequence-independent rigid-body protein docking across a wide range of symmetric architectures that is easily customizable for further development. RPXDock uses an efficient hierarchical search and a residue-pair transform (RPX) scoring method to rapidly search through multidimensional docking space. We describe the structure of the software, provide practical guidelines for its use, and describe the available functionalities including a variety of score functions and filtering tools that can be used to guide and refine docking results towards desired configurations.
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spelling pubmed-102376592023-06-03 Fast and versatile sequence-independent protein docking for nanomaterials design using RPXDock Sheffler, William Yang, Erin C. Dowling, Quinton Hsia, Yang Fries, Chelsea N. Stanislaw, Jenna Langowski, Mark D. Brandys, Marisa Li, Zhe Skotheim, Rebecca Borst, Andrew J. Khmelinskaia, Alena King, Neil P. Baker, David PLoS Comput Biol Research Article Computationally designed multi-subunit assemblies have shown considerable promise for a variety of applications, including a new generation of potent vaccines. One of the major routes to such materials is rigid body sequence-independent docking of cyclic oligomers into architectures with point group or lattice symmetries. Current methods for docking and designing such assemblies are tailored to specific classes of symmetry and are difficult to modify for novel applications. Here we describe RPXDock, a fast, flexible, and modular software package for sequence-independent rigid-body protein docking across a wide range of symmetric architectures that is easily customizable for further development. RPXDock uses an efficient hierarchical search and a residue-pair transform (RPX) scoring method to rapidly search through multidimensional docking space. We describe the structure of the software, provide practical guidelines for its use, and describe the available functionalities including a variety of score functions and filtering tools that can be used to guide and refine docking results towards desired configurations. Public Library of Science 2023-05-22 /pmc/articles/PMC10237659/ /pubmed/37216343 http://dx.doi.org/10.1371/journal.pcbi.1010680 Text en © 2023 Sheffler et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Sheffler, William
Yang, Erin C.
Dowling, Quinton
Hsia, Yang
Fries, Chelsea N.
Stanislaw, Jenna
Langowski, Mark D.
Brandys, Marisa
Li, Zhe
Skotheim, Rebecca
Borst, Andrew J.
Khmelinskaia, Alena
King, Neil P.
Baker, David
Fast and versatile sequence-independent protein docking for nanomaterials design using RPXDock
title Fast and versatile sequence-independent protein docking for nanomaterials design using RPXDock
title_full Fast and versatile sequence-independent protein docking for nanomaterials design using RPXDock
title_fullStr Fast and versatile sequence-independent protein docking for nanomaterials design using RPXDock
title_full_unstemmed Fast and versatile sequence-independent protein docking for nanomaterials design using RPXDock
title_short Fast and versatile sequence-independent protein docking for nanomaterials design using RPXDock
title_sort fast and versatile sequence-independent protein docking for nanomaterials design using rpxdock
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10237659/
https://www.ncbi.nlm.nih.gov/pubmed/37216343
http://dx.doi.org/10.1371/journal.pcbi.1010680
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