ArticleCommunications biology2023
Protein structure and folding pathway prediction based on remote homologs recognition using PAthreader.
Article in Communications biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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21 citing papers in PubMed, 51 citations in OpenAlex.
- MultilevelCurrent research in structural biology · 2026Article
- AI-Predicted Model-Guided Rebuilding of the Experimental Structure of Mouse δ-Aminolevulinic Acid Dehydratase.International journal of molecular sciences · 2026Article
- Efficient global accuracy estimation for protein complex structural models using multi-view representation learning.Cell reports methods · 2026Article
- Unavailability of experimental 3D structural data on protein folding dynamics and necessity for a new generation of structure prediction methods in this context.Bioinformatics (Oxford, England) · 2026Article
- Multiple conformational states assembly of multidomain proteins using evolutionary algorithm based on structural analogues and sequential homologues.Fundamental research · 2026Article
- Multimodal pre-training models of molecular representation for drug discovery.National science review · 2026Review
- A Computational Perspective to Intermolecular Interactions and the Role of the Solvent on Regulating Protein Properties.Chemical reviews · 2025Review
- MEGDTA: multi-modal drug-target affinity prediction based on protein three-dimensional structure and ensemble graph neural network.BMC genomics · 2025Article
- Multimeric protein interaction and complex prediction: Structure, dynamics and function.Computational and structural biotechnology journal · 2025Review
- Detection of Ethylene Signaling Using Bioinformatics Tools in Plants.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Recent advances and challenges in protein complex model accuracy estimation.Computational and structural biotechnology journal · 2024Review
- Protein Multiple Conformation Prediction Using Multi-Objective Evolution Algorithm.Interdisciplinary sciences, computational life sciences · 2024Article
- FoldPAthreader: predicting protein folding pathway using a novel folding force field model derived from known protein universe.Genome biology · 2024Article
- SPDesign: protein sequence designer based on structural sequence profile using ultrafast shape recognition.Briefings in bioinformatics · 2024Article
- Recent Advances in Protein Folding Pathway Prediction through Computational Methods.Current medicinal chemistry · 2024Review
- Keeping it in the family: using protein family templates to rescue low confidence AlphaFold2 models.Bioinformatics advances · 2024Article
- Multi-domain and complex protein structure prediction using inter-domain interactions from deep learning.Communications biology · 2023Article
- Assessing protein model quality based on deep graph coupled networks using protein language model.Briefings in bioinformatics · 2023Article
- SeqPredNN: a neural network that generates protein sequences that fold into specified tertiary structures.BMC bioinformatics · 2023Article
- Pathfinder: Protein folding pathway prediction based on conformational sampling.PLoS computational biology · 2023Article
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Authors and funding
6 authors at 2 institutions in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
Recognition of remote homologous structures is a necessary module in AlphaFold2 and is also essential for the exploration of protein folding pathways. Here, we propose a method, PAthreader, to recognize remote templates and explore folding pathways. Firstly, we design a three-track alignment between predicted distance profiles and structure profiles extracted from PDB and AlphaFold DB, to improve the recognition accuracy of remote templates. Secondly, we improve the performance of AlphaFold2 using the templates identified by PAthreader. Thirdly, we explore protein folding pathways based on our conjecture that dynamic folding information of protein is implicitly contained in its remote homologs. The results show that the average accuracy of PAthreader templates is 11.6% higher than that of HHsearch. In terms of structure modelling, PAthreader outperform AlphaFold2 and ranks first on the CAMEO blind test for the latest three months. Furthermore, we predict protein folding pathways for 37 proteins, in which the results of 7 proteins are almost consistent with those of biological experiments, and the other 30 human proteins have yet to be verified by biological experiments, revealing that folding information can be exploited from remote homologous structures.
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