ThreaDomEx: a unified platform for predicting continuous and discontinuous protein domains by multiple-threading and segment assembly

Nucleic Acids Research
Yan WangYang Zhang

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 accu...Continue Reading

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Citations

May 10, 2019·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Gideon K GogoviEstela Blaisten-Barojas
Jan 12, 2020·Proceedings of the National Academy of Sciences of the United States of America·Oleg KlykovRichard A Scheltema
Jul 8, 2020·Applied and Environmental Microbiology·Ting YangWei-Dong Lu
Jul 28, 2020·International Journal of Molecular Sciences·Michela GambinoLone Brøndsted
Aug 28, 2020·Frontiers in Molecular Biosciences·Anwar Ullah, Rehana Masood
Feb 22, 2021·Toxicon : Official Journal of the International Society on Toxinology·Amit AhujaVishal Singh Somvanshi
Mar 9, 2021·Computational and Structural Biotechnology Journal·Yan WangZhidong Xue
Aug 21, 2019·Future Generations Computer Systems : FGCS·Wei ZhengYang Zhang
Aug 24, 2018··Amarda ShehuFahad Almsned

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