ReviewNature protocols2022
Integrative structural modeling of macromolecular complexes using Assembline.
Review in Nature protocols, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed, 62 citations in OpenAlex.
- A conserved GTPase complex gates exocytosis for defence and parasitism across alveolates.Nature microbiology · 2026Article
- Interface swapping orchestrates carbon transfer in the archaeal acetyl-CoA decarbonylase/synthase.bioRxiv : the preprint server for biology · 2026Article
- In situ architecture of the nuclear pore complex of the higher plant Arabidopsis thaliana.Nature plants · 2025Article
- A deep learning method for predicting interactions for intrinsically disordered regions of proteins.bioRxiv : the preprint server for biology · 2025Article
- Tutorial on integrative spatiotemporal modeling by integrative modeling platform.Protein science : a publication of the Protein Society · 2025Article
- Integrative spatiotemporal modeling of biomolecular processes: Application to the assembly of the nuclear pore complex.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- An outlook on structural biology after AlphaFold: tools, limits and perspectives.FEBS open bio · 2025Review
- Frontiers in integrative structural modeling of macromolecular assemblies.QRB discovery · 2025Review
- DiffModeler: large macromolecular structure modeling for cryo-EM maps using a diffusion model.Nature methods · 2024Article
- Article
- DomainFit: Identification of protein domains in cryo-EM maps at intermediate resolution using AlphaFold2-predicted models.Structure (London, England : 1993) · 2024Article
- Integrative spatiotemporal modeling of biomolecular processes: application to the assembly of the Nuclear Pore Complex.bioRxiv : the preprint server for biology · 2024Article
- Chemical cross-linking and mass spectrometry enabled systems-level structural biology.Current opinion in structural biology · 2024Review
- IDRWalker: A Random Walk Based Tool for Generating Intrinsically Disordered Regions in Large Protein Complexes.ACS omega · 2024Article
- The palisade layer of the poxvirus core is composed of flexible A10 trimers.Nature structural & molecular biology · 2024Article
- CombFold: predicting structures of large protein assemblies using a combinatorial assembly algorithm and AlphaFold2.Nature methods · 2024Article
- DiffModeler: Large Macromolecular Structure Modeling in Low-Resolution Cryo-EM Maps Using Diffusion Model.bioRxiv : the preprint server for biology · 2024Article
- MoDAFold: a strategy for predicting the structure of missense mutant protein based on AlphaFold2 and molecular dynamics.Briefings in bioinformatics · 2024Article
- DomainFit: Identification of Protein Domains in cryo-EM maps at Intermediate Resolution using AlphaFold2-predicted Models.bioRxiv : the preprint server for biology · 2023Article
- Simulating structurally variable nuclear pore complexes for microscopy.Bioinformatics (Oxford, England) · 2023Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Integrative modeling enables structure determination of macromolecular complexes by combining data from multiple experimental sources such as X-ray crystallography, electron microscopy or cross-linking mass spectrometry. It is particularly useful for complexes not amenable to high-resolution electron microscopy-complexes that are flexible, heterogeneous or imaged in cells with cryo-electron tomography. We have recently developed an integrative modeling protocol that allowed us to model multi-megadalton complexes as large as the nuclear pore complex. Here, we describe the Assembline software package, which combines multiple programs and libraries with our own algorithms in a streamlined modeling pipeline. Assembline builds ensembles of models satisfying data from atomic structures or homology models, electron microscopy maps and other experimental data, and provides tools for their analysis. Compared with other methods, Assembline enables efficient sampling of conformational space through a multistep procedure, provides new modeling restraints and includes a unique configuration system for setting up the modeling project. Our protocol achieves exhaustive sampling in less than 100-1,000 CPU-hours even for complexes in the megadalton range. For larger complexes, resources available in institutional or public computer clusters are needed and sufficient to run the protocol. We also provide step-by-step instructions for preparing the input, running the core modeling steps and assessing modeling performance at any stage.
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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.