ArticlePLoS computational biology2023
Fast and versatile sequence-independent protein docking for nanomaterials design using RPXDock.
Article in PLoS computational biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Review
- Review
- Self-assembling protein cages: from coiled-coil module to machine learning-drivenMaterials advances · 2026Review
- De novo design of protein nanoparticles with integrated functional motifs.bioRxiv : the preprint server for biology · 2026Article
- De novo design of light-responsive protein-protein interactions enables reversible formation of protein assemblies.Nature chemistry · 2025Article
- From sequence to scaffold: Computational design of protein nanoparticle vaccines from AlphaFold2-predicted building blocks.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Computational design of bifaceted protein nanomaterials.Nature materials · 2025Article
- Bond-centric modular design of protein assemblies.Nature materials · 2025Article
- Computational design of non-porous pH-responsive antibody nanoparticles.Nature structural & molecular biology · 2024Article
- Custom protein nanoparticles for targeted drug delivery.Nature structural & molecular biology · 2024Article
- Article
- Rationally seeded computational protein design of ɑ-helical barrels.Nature chemical biology · 2024Article
- Article
- De novo design of proteins housing excitonically coupled chlorophyll special pairs.Nature chemical biology · 2024Article
- Rapid and automated design of two-component protein nanomaterials using ProteinMPNN.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Article
- Sparks of function by de novo protein design.Nature biotechnology · 2024Review
- Accurate computational design of three-dimensional protein crystals.Nature materials · 2023Article
- Structural Optimization Design of Microfluidic Chips Based on Fast Sequence Pair Algorithm.Micromachines · 2023Article
- Article
Corrections and comments
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Authors and funding
14 authors.
Funding
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.