8FWD

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

Summary for 8FWD

• Entry DOI: 10.2210/pdb8fwd/pdb
• EMDB information: 29502
• Descriptor: O43-rpxdoc-EK1_A, O43-rpxdoc-EK1_B (2 entities in total)
• Functional Keywords: octahedra, oligomer, de novo design, rosetta, cryoem, interface, de novo protein
• Biological source: synthetic construct; More
• Total number of polymer chains: 48
• Total formula weight: 1005427.78

Authors

Skotheim, R.,Borst, A.J.,Baker, D. (deposition date: 2023-01-20, release date: 2023-05-10, Last modification date: 2025-06-04)

Primary citation

Sheffler, W.,Yang, E.C.,Dowling, Q.,Hsia, Y.,Fries, C.N.,Stanislaw, J.,Langowski, M.D.,Brandys, M.,Li, Z.,Skotheim, R.,Borst, A.J.,Khmelinskaia, A.,King, N.P.,Baker, D.
Fast and versatile sequence-independent protein docking for nanomaterials design using RPXDock.
Plos Comput.Biol., 19:e1010680-e1010680, 2023

PubMed Abstract: 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.

PubMed: 37216343
DOI: 10.1371/journal.pcbi.1010680

Experimental method

ELECTRON MICROSCOPY (3.67 Å)