Cargando…
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...
Autores principales: | , , , , , , , , , , , , , |
---|---|
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 |
_version_ | 1785053191569670144 |
---|---|
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. |
format | Online Article Text |
id | pubmed-10237659 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
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 |
work_keys_str_mv | AT shefflerwilliam fastandversatilesequenceindependentproteindockingfornanomaterialsdesignusingrpxdock AT yangerinc fastandversatilesequenceindependentproteindockingfornanomaterialsdesignusingrpxdock AT dowlingquinton fastandversatilesequenceindependentproteindockingfornanomaterialsdesignusingrpxdock AT hsiayang fastandversatilesequenceindependentproteindockingfornanomaterialsdesignusingrpxdock AT frieschelsean fastandversatilesequenceindependentproteindockingfornanomaterialsdesignusingrpxdock AT stanislawjenna fastandversatilesequenceindependentproteindockingfornanomaterialsdesignusingrpxdock AT langowskimarkd fastandversatilesequenceindependentproteindockingfornanomaterialsdesignusingrpxdock AT brandysmarisa fastandversatilesequenceindependentproteindockingfornanomaterialsdesignusingrpxdock AT lizhe fastandversatilesequenceindependentproteindockingfornanomaterialsdesignusingrpxdock AT skotheimrebecca fastandversatilesequenceindependentproteindockingfornanomaterialsdesignusingrpxdock AT borstandrewj fastandversatilesequenceindependentproteindockingfornanomaterialsdesignusingrpxdock AT khmelinskaiaalena fastandversatilesequenceindependentproteindockingfornanomaterialsdesignusingrpxdock AT kingneilp fastandversatilesequenceindependentproteindockingfornanomaterialsdesignusingrpxdock AT bakerdavid fastandversatilesequenceindependentproteindockingfornanomaterialsdesignusingrpxdock |