ArticleNature protocols2018
Structural prediction of protein models using distance restraints derived from cross-linking mass spectrometry data.
Article in Nature protocols, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 38 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
38 citing papers in PubMed.
- Incorporating Surfaced-Induced Dissociation Mass Spectrometry Data into an AlphaFold-derived deep learning network improves protein structure prediction.bioRxiv : the preprint server for biology · 2026Article
- Integrative Structural Modeling of Intrinsically Disordered Regions in a Human HDAC2 Chromatin Remodeling Complex.bioRxiv : the preprint server for biology · 2026Article
- Structural mass spectrometry techniques for characterisation of plant and algal proteins.The Plant journal : for cell and molecular biology · 2026Review
- Elucidating PTEN conformational dynamics and phosphatase regulation via integrative modeling and mutation prediction.Structure (London, England : 1993) · 2025Article
- Mapping the interaction surface between CaNature communications · 2025Article
- Integrated structural model of the palladin-actin complex using XL-MS, docking, NMR, and SAXS.Protein science : a publication of the Protein Society · 2025Article
- Energy Resolved Mass Spectrometry Data from Surfaced Induced Dissociation Improves Prediction of Protein Complex Structure.Analytical chemistry · 2025Article
- Rational Modification of a Cross-Linker for Improved Flexible Protein Structure Modeling.Analytical chemistry · 2025Article
- Native Mass Spectrometry Reveals Binding Interactions of SARS-CoV-2 PLpro with Inhibitors and Cellular Targets.ACS infectious diseases · 2024Article
- A Tutorial Review of Labeling Methods in Mass Spectrometry-Based Quantitative Proteomics.ACS measurement science au · 2024Review
- Assessment of Two Restraint Potentials for Coarse-Grained Chemical-Cross-Link-Assisted Modeling of Protein Structures.Journal of chemical information and modeling · 2024Article
- The LIKE SEX FOUR 1-malate dehydrogenase complex functions as a scaffold to recruit β-amylase to promote starch degradation.The Plant cell · 2023Article
- Higher-Order Structural Organization of the Mitochondrial Proteome Charted by In Situ Cross-Linking Mass Spectrometry.Molecular & cellular proteomics : MCP · 2023Article
- Systematic conformation-to-phenotype mapping via limited deep sequencing of proteins.Molecular cell · 2023Article
- Article
- Structural insights into DNA NCell discovery · 2023Article
- Binding stoichiometry and structural model of the HIV-1 Rev/importin β complex.Life science alliance · 2022Article
- Shape shifting: The multiple conformational substates of the PTEN N-terminal PIPProtein science : a publication of the Protein Society · 2022Article
- In-Cell Labeling and Mass Spectrometry for Systems-Level Structural Biology.Chemical reviews · 2022Review
- Accurate and Automated High-Coverage Identification of Chemically Cross-Linked Peptides with MaxLynx.Analytical chemistry · 2022Article
Corrections and comments
- Commented on by
- Erratum issued
Authors and funding
9 authors.
Funding
Abstract
This protocol describes a workflow for creating structural models of proteins or protein complexes using distance restraints derived from cross-linking mass spectrometry experiments. The distance restraints are used (i) to adjust preliminary models that are calculated on the basis of a homologous template and primary sequence, and (ii) to select the model that is in best agreement with the experimental data. In the case of protein complexes, the cross-linking data are further used to dock the subunits to one another to generate models of the interacting proteins. Predicting models in such a manner has the potential to indicate multiple conformations and dynamic changes that occur in solution. This modeling protocol is compatible with many cross-linking workflows and uses open-source programs or programs that are free for academic users and do not require expertise in computational modeling. This protocol is an excellent additional application with which to use cross-linking results for building structural models of proteins. The established protocol is expected to take 6-12 d to complete, depending on the size of the proteins and the complexity of the cross-linking data.
Indexed as
Identifiers
What OpenQuestion holds
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.