ArticlePLoS computational biology2018
Modeling the assembly order of multimeric heteroprotein complexes.
Article in PLoS computational biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 37 citations in OpenAlex.
- Stepwise order in protein complex assembly: approaches and emerging themes.Open biology · 2025Review
- Assessment of Protein-Protein Docking Models Using Deep Learning.Methods in molecular biology (Clifton, N.J.) · 2024Review
- A hierarchical assembly pathway directs the unique subunit arrangement of TRiC/CCT.Molecular cell · 2023Article
- Simulation toolkits at the molecular scale for trans-scale thermal signaling.Computational and structural biotechnology journal · 2023Review
- Review
- Genome‑wide identification of CAMTA gene family members in rice (Oryza sativa L.) and in silico study on their versatility in respect to gene expression and promoter structure.Functional & integrative genomics · 2022Article
- Bioengineering and computational analysis of programmed cell death ligand-1 monoclonal antibody.Frontiers in immunology · 2022Article
- RL-MLZerD: Multimeric protein docking using reinforcement learning.Frontiers in molecular biosciences · 2022Article
- LZerD webserver for pairwise and multiple protein-protein docking.Nucleic acids research · 2021Article
- Article
- LZerD Protein-Protein Docking Webserver Enhanced WithFrontiers in molecular biosciences · 2021Review
- The complexity of protein interactions unravelled from structural disorder.PLoS computational biology · 2021Article
- Protein Docking Model Evaluation by Graph Neural Networks.Frontiers in molecular biosciences · 2021Article
- Computational structure modeling for diverse categories of macromolecular interactions.Current opinion in structural biology · 2020Review
- Protein docking model evaluation by 3D deep convolutional neural networks.Bioinformatics (Oxford, England) · 2020Article
- Evolution of interface binding strengths in simplified model of protein quaternary structure.PLoS computational biology · 2019Article
- SWISS-MODEL: homology modelling of protein structures and complexes.Nucleic acids research · 2018Article
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Authors and funding
8 authors at 2 institutions in 1 country.
Funding
Abstract
Protein-protein interactions are the cornerstone of numerous biological processes. Although an increasing number of protein complex structures have been determined using experimental methods, relatively fewer studies have been performed to determine the assembly order of complexes. In addition to the insights into the molecular mechanisms of biological function provided by the structure of a complex, knowing the assembly order is important for understanding the process of complex formation. Assembly order is also practically useful for constructing subcomplexes as a step toward solving the entire complex experimentally, designing artificial protein complexes, and developing drugs that interrupt a critical step in the complex assembly. There are several experimental methods for determining the assembly order of complexes; however, these techniques are resource-intensive. Here, we present a computational method that predicts the assembly order of protein complexes by building the complex structure. The method, named Path-LzerD, uses a multimeric protein docking algorithm that assembles a protein complex structure from individual subunit structures and predicts assembly order by observing the simulated assembly process of the complex. Benchmarked on a dataset of complexes with experimental evidence of assembly order, Path-LZerD was successful in predicting the assembly pathway for the majority of the cases. Moreover, when compared with a simple approach that infers the assembly path from the buried surface area of subunits in the native complex, Path-LZerD has the strong advantage that it can be used for cases where the complex structure is not known. The path prediction accuracy decreased when starting from unbound monomers, particularly for larger complexes of five or more subunits, for which only a part of the assembly path was correctly identified. As the first method of its kind, Path-LZerD opens a new area of computational protein structure modeling and will be an indispensable approach for studying protein complexes.
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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.