ArticleProteins2021
Protein oligomer modeling guided by predicted interchain contacts in CASP14.
Article in Proteins, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Multimeric protein interaction and complex prediction: Structure, dynamics and function.Computational and structural biotechnology journal · 2025Review
- Review and Comparative Analysis of Methods and Advancements in Predicting Protein Complex Structure.Interdisciplinary sciences, computational life sciences · 2024Review
- Combining small angle X-ray scattering (SAXS) with protein structure predictions to characterize conformations in solution.Methods in enzymology · 2023Article
- Improvement of protein tertiary and quaternary structure predictions using the ReFOLD refinement method and the AlphaFold2 recycling process.Bioinformatics advances · 2023Article
- Protein Function Analysis through Machine Learning.Biomolecules · 2022Review
- Modeling of protein conformational changes with Rosetta guided by limited experimental data.Structure (London, England : 1993) · 2022Article
- Application of Homology Modeling by Enhanced Profile-Profile Alignment and Flexible-Fitting Simulation to Cryo-EM Based Structure Determination.International journal of molecular sciences · 2022Article
- AlphaFold Models of Small Proteins Rival the Accuracy of Solution NMR Structures.Frontiers in molecular biosciences · 2022Article
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Authors and funding
5 authors.
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Abstract
For CASP14, we developed deep learning-based methods for predicting homo-oligomeric and hetero-oligomeric contacts and used them for oligomer modeling. To build structure models, we developed an oligomer structure generation method that utilizes predicted interchain contacts to guide iterative restrained minimization from random backbone structures. We supplemented this gradient-based fold-and-dock method with template-based and ab initio docking approaches using deep learning-based subunit predictions on 29 assembly targets. These methods produced oligomer models with summed Z-scores 5.5 units higher than the next best group, with the fold-and-dock method having the best relative performance. Over the eight targets for which this method was used, the best of the five submitted models had average oligomer TM-score of 0.71 (average oligomer TM-score of the next best group: 0.64), and explicit modeling of inter-subunit interactions improved modeling of six out of 40 individual domains (ΔGDT-TS > 2.0).
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.