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000893374 1001_ $$0P:(DE-HGF)0$$aMulnaes, Daniel$$b0
000893374 245__ $$aTopDomain: Exhaustive Protein Domain Boundary Metaprediction Combining Multisource Information and Deep Learning
000893374 260__ $$aWashington, DC$$c2021
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000893374 520__ $$aProtein domains are independent, functional, and stable structural units of proteins. Accurate protein domain boundary prediction plays an important role in understanding protein structure and evolution, as well as for protein structure prediction. Current domain boundary prediction methods differ in terms of boundary definition, methodology, and training databases resulting in disparate performance for different proteins. We developed TopDomain, an exhaustive metapredictor, that uses deep neural networks to combine multisource information from sequence- and homology-based features of over 50 primary predictors. For this purpose, we developed a new domain boundary data set termed the TopDomain data set, in which the true annotations are informed by SCOPe annotations, structural domain parsers, human inspection, and deep learning. We benchmark TopDomain against 2484 targets with 3354 boundaries from the TopDomain test set and achieve F1 scores of 78.4% and 73.8% for multidomain boundary prediction within ±20 residues and ±10 residues of the true boundary, respectively. When examined on targets from CASP11-13 competitions, TopDomain achieves F1 scores of 47.5% and 42.8% for multidomain proteins. TopDomain significantly outperforms 15 widely used, state-of-the-art ab initio and homology-based domain boundary predictors. Finally, we implemented TopDomainTMC, which accurately predicts whether domain parsing is necessary for the target protein.
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000893374 7001_ $$0P:(DE-HGF)0$$aGolchin, Pegah$$b1
000893374 7001_ $$0P:(DE-HGF)0$$aKoenig, Filip$$b2
000893374 7001_ $$0P:(DE-Juel1)172663$$aGohlke, Holger$$b3$$eCorresponding author
000893374 773__ $$0PERI:(DE-600)2166976-4$$a10.1021/acs.jctc.1c00129$$gp. acs.jctc.1c00129$$n7$$p4599–4613$$tJournal of chemical theory and computation$$v17$$x1549-9626$$y2021
000893374 8564_ $$uhttps://juser.fz-juelich.de/record/893374/files/acs.jctc.1c00129.pdf
000893374 8564_ $$uhttps://juser.fz-juelich.de/record/893374/files/TopDomain_Ms_JCTC_rev_final.pdf$$yPublished on 2021-06-23. Available in OpenAccess from 2022-06-23.
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