ArticleProceedings of the National Academy of Sciences of the United States of America2019
Assembling multidomain protein structures through analogous global structural alignments.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 63 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
63 citing papers in PubMed.
- MultilevelCurrent research in structural biology · 2026Article
- Candidate compounds associated with sourness and astringency in Corni Fructus: an integrated analysis of chemical profiles, sensory evaluation, and molecular docking.Food chemistry: X · 2026Article
- Identifying potential binding sites for complex formation between Tyrosyl-DNA phosphodiesterase 1 and poly [ADP-ribose] polymerase 1.Physical chemistry chemical physics : PCCP · 2026Article
- A graphic and command line protocol for quick and accurate comparisons of protein and nucleic acid structures with US-align.Nature protocols · 2026Review
- AI-driven insights into protein misfolding and innate immunity in neurodegenerative diseases.Frontiers in immunology · 2026Review
- Multimodal pre-training models of molecular representation for drug discovery.National science review · 2026Review
- Molecular Evolution of Paralogous Cold Shock Proteins in E. coli: A Study of Asymmetric Divergence and Protein Functional Networks.Molecular biotechnology · 2026Article
- Multiple conformational states assembly of multidomain proteins using evolutionary algorithm based on structural analogues and sequential homologues.Fundamental research · 2026Article
- Adjacent domains drive the emergence of misfolded intermediates in the folding pathway of the PDZ4 from MAGI1.BBA advances · 2026Article
- A Comprehensive Review on Homology Modelling in Drug Development: Methodologies, Tools, and Evaluation.Mini reviews in medicinal chemistry · 2026Review
- EWS-RNA Binding Protein 1: Structural Insights into Ewing Sarcoma by Conformational Dynamics Investigations.Current cancer drug targets · 2026Article
- MDM2-P53-V-ATPases axis driven by dehydroevodiamine to fight intracellular bacterial infection.Communications biology · 2025Article
- SPAED: harnessing AlphaFold output for accurate segmentation of phage endolysin domains.Bioinformatics (Oxford, England) · 2025Article
- Advances in the chemical synthesis of human proteoforms.Science China. Life sciences · 2025Review
- DEMO-EMol: modeling protein-nucleic acid complex structures from cryo-EM maps by coupling chain assembly with map segmentation.Nucleic acids research · 2025Article
- Putative type III effector SkP48 of Bradyrhizobium sp. DOA9 encoding a SUMO protease blocks nodulation in Vigna radiata.Scientific reports · 2025Article
- M-DeepAssembly: enhanced DeepAssembly based on multi-objective multi-domain protein conformation sampling.BMC bioinformatics · 2025Article
- A Novel Phosphorylated Tau Conformer Implicated in the Tauopathy Pathogenesis of Human Neurons.Biomolecules · 2025Article
- Expanding kinetoplastid genome annotation through protein structure comparison.PLoS pathogens · 2025Article
- Characterization of the host specificity of the SH3 cell wall binding domain of the staphylococcal phage 88 endolysin.Archives of microbiology · 2025Article
3 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
Most proteins exist with multiple domains in cells for cooperative functionality. However, structural biology and protein folding methods are often optimized for single-domain structures, resulting in a rapidly growing gap between the improved capability for tertiary structure determination and high demand for multidomain structure models. We have developed a pipeline, termed DEMO, for constructing multidomain protein structures by docking-based domain assembly simulations, with interdomain orientations determined by the distance profiles from analogous templates as detected through domain-level structure alignments. The pipeline was tested on a comprehensive benchmark set of 356 proteins consisting of 2-7 continuous and discontinuous domains, for which DEMO generated models with correct global fold (TM-score > 0.5) for 86% of cases with continuous domains and for 100% of cases with discontinuous domain structures, starting from randomly oriented target-domain structures. DEMO was also applied to reassemble multidomain targets in the CASP12 and CASP13 experiments using domain structures excised from the top server predictions, where the full-length DEMO models showed a significantly improved quality over the original server models. Finally, sparse restraints of mass spectrometry-generated cross-linking data and cryo-EM density maps are incorporated into DEMO, resulting in improvements in the average TM-score by 6.3% and 12.5%, respectively. The results demonstrate an efficient approach to assembling multidomain structures, which can be easily used for automated, genome-scale multidomain protein structure assembly.
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.