ArticleNucleic acids research2022
DEMO2: Assemble multi-domain protein structures by coupling analogous template alignments with deep-learning inter-domain restraint prediction.
Article in Nucleic acids research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- MultilevelCurrent research in structural biology · 2026Article
- Deep-learning-based single-domain and multidomain protein structure prediction with D-I-TASSER.Nature biotechnology · 2026Article
- Multiple conformational states assembly of multidomain proteins using evolutionary algorithm based on structural analogues and sequential homologues.Fundamental research · 2026Article
- Accelerated discovery and miniaturization of novel single-stranded cytidine deaminases.Nucleic acids research · 2024Article
- Recent Progress of Protein Tertiary Structure Prediction.Molecules (Basel, Switzerland) · 2024Review
- Modeling and Analysis of HIV-1 Pol Polyprotein as a Case Study for Predicting Large Polyprotein Structures.International journal of molecular sciences · 2024Article
- DEMO-EM2: assembling protein complex structures from cryo-EM maps through intertwined chain and domain fitting.Briefings in bioinformatics · 2024Article
- Creation of a Curated Database of Experimentally Determined Human Protein Structures for the Identification of Its Targetome.Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing · 2024Article
- Recent Advances in Protein Folding Pathway Prediction through Computational Methods.Current medicinal chemistry · 2024Review
- Multi-domain and complex protein structure prediction using inter-domain interactions from deep learning.Communications biology · 2023Article
- Article
- Narrow funnel-like interaction energy distribution is an indicator of specific protein interaction partner.iScience · 2023Article
- Protein structure and folding pathway prediction based on remote homologs recognition using PAthreader.Communications biology · 2023Article
- Structural modelling of human complement FHR1 and two of its synthetic derivatives provides insight into their in-vivo functions.Computational and structural biotechnology journal · 2023Article
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6 authors.
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Abstract
Most proteins in nature contain multiple folding units (or domains). The revolutionary success of AlphaFold2 in single-domain structure prediction showed potential to extend deep-learning techniques for multi-domain structure modeling. This work presents a significantly improved method, DEMO2, which integrates analogous template structural alignments with deep-learning techniques for high-accuracy domain structure assembly. Starting from individual domain models, inter-domain spatial restraints are first predicted with deep residual convolutional networks, where full-length structure models are assembled using L-BFGS simulations under the guidance of a hybrid energy function combining deep-learning restraints and analogous multi-domain template alignments searched from the PDB. The output of DEMO2 contains deep-learning inter-domain restraints, top-ranked multi-domain structure templates, and up to five full-length structure models. DEMO2 was tested on a large-scale benchmark and the blind CASP14 experiment, where DEMO2 was shown to significantly outperform its predecessor and the state-of-the-art protein structure prediction methods. By integrating with new deep-learning techniques, DEMO2 should help fill the rapidly increasing gap between the improved ability of tertiary structure determination and the high demand for the high-quality multi-domain protein structures. The DEMO2 server is available at https://zhanggroup.org/DEMO/.
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