ArticleNucleic acids research2017
ThreaDomEx: a unified platform for predicting continuous and discontinuous protein domains by multiple-threading and segment assembly.
Article in Nucleic acids research, 2017. 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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17 citing papers in PubMed.
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- Metagenomic domain substitution for the high-throughput modification of nonribosomal peptides.Nature chemical biology · 2024Article
- I-TASSER-MTD: a deep-learning-based platform for multi-domain protein structure and function prediction.Nature protocols · 2022Review
- Progressive assembly of multi-domain protein structures from cryo-EM density maps.Nature computational science · 2022Article
- In Silico Screening and In Vitro Assessment of Natural Products with Anti-Virulence Activity againstMolecules (Basel, Switzerland) · 2021Article
- Probabilistic divergence of a template-based modelling methodology from the ideal protocol.Journal of molecular modeling · 2021Article
- Protein domain identification methods and online resources.Computational and structural biotechnology journal · 2021Review
- Role ofApplied and environmental microbiology · 2020Article
- Phage S144, A New Polyvalent Phage InfectingInternational journal of molecular sciences · 2020Article
- FUpred: detecting protein domains through deep-learning-based contact map prediction.Bioinformatics (Oxford, England) · 2020Article
- Functional Characterization of Alr0765, A Hypothetical Protein fromCurrent genomics · 2020Article
- Missing regions within the molecular architecture of human fibrin clots structurally resolved by XL-MS and integrative structural modeling.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- The Sequence and Three-Dimensional Structure Characterization of Snake Venom Phospholipases B.Frontiers in molecular biosciences · 2020Article
- I-TASSER gateway: A protein structure and function prediction server powered by XSEDE.Future generations computer systems : FGCS · 2019Article
- Modeling the Tertiary Structure of the Rift Valley Fever Virus L Protein.Molecules (Basel, Switzerland) · 2019Article
- Protocol for analyzing protein ensemble structures from chemical cross-links using DynaXL.Biophysics reports · 2017Article
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6 authors.
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Abstract
We develop a hierarchical pipeline, ThreaDomEx, for both continuous domain (CD) and discontinuous domain (DCD) structure predictions. Starting from a query sequence, ThreaDomEx first threads it through the PDB to identify multiple structure templates, where a profile of domain conservation score (DC-score) is derived for domain-segment assignment. To further detect DCDs that consist of separated segments along the sequence, a boundary-clustering algorithm is used to refine the DCD-linker locations. In case that the templates do not contain DCDs, a domain-segment assembly process, guided by symmetry comparison, is applied for further DCD detections. ThreaDomEx was tested a set of 1111 proteins and achieved a normalized domain overlap score of 89.3% compared to experimental data, which is significantly higher than other state-of-the-art methods. It also recalls 26.7% of DCDs with 72.7% precision on the proteins for which threading failed to detect any DCDs. The server provides facilities for users to interactively refine the domain models by adjusting DC-score threshold, deleting and adding domain linkers, and assembling domain segments, which are particularly helpful for the hard targets for which current methods have a low accuracy while human-expert knowledge and experimental insights can be used for refining models. ThreaDomEX server is available at http://zhanglab.ccmb.med.umich.edu/ThreaDomEx.
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