ArticleBioinformatics advances2023
Improvement of protein tertiary and quaternary structure predictions using the ReFOLD refinement method and the AlphaFold2 recycling process.
Article in Bioinformatics advances, 2023. 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, 20 citations in OpenAlex.
- In Silico Design and Characterization of the Essential Outer-Membrane Lipoprotein LolB-Derived Multi-Epitope Vaccine Candidate AgainstMethods and protocols · 2026Article
- Computational Development of Multi-Epitope Reovirus Vaccine with Potent Predicted Binding to TLR2 and TLR4.Pharmaceuticals (Basel, Switzerland) · 2025Article
- Prediction and quality assessment of protein quaternary structure models using the MultiFOLD2 and ModFOLDdock2 servers.Nucleic acids research · 2025Article
- Stability and functional consequences of disulfide bond engineering in Aspergillus flavus uricase.Scientific reports · 2025Article
- Novel MRSA-targeting phage MetB16: Genomic features, structural insights, and therapeutic applications.Turkish journal of biology = Turk biyoloji dergisi · 2025Article
- Epigallocatechin-3-gallate: a multi-target bioactive molecule derived from green tea against Oropouche virus-a computational approach to host-pathogen network modulation.Frontiers in chemistry · 2025Article
- Dissecting AlphaFold2's capabilities with limited sequence information.Bioinformatics advances · 2025Article
- PD-1 is conserved from sharks to humans: new insights into PD-1, PD-L1, PD-L2, and SHP-2 evolution.Frontiers in immunology · 2025Article
- Interpreting forces as deep learning gradients improves quality of predicted protein structures.Biophysical journal · 2024Article
- The early communication stages between serine proteases and enterovirus capsids in the race for viral disintegration.Communications biology · 2024Article
- Benchmarking of AlphaFold2 accuracy self-estimates as indicators of empirical model quality and ranking: a comparison with independent model quality assessment programmes.Bioinformatics (Oxford, England) · 2024Article
- Efficient Refinement of Complex Structures of Flexible Histone Peptides Using Post-Docking Molecular Dynamics Protocols.International journal of molecular sciences · 2024Article
- NuFold: A Novel Tertiary RNA Structure Prediction Method Using Deep Learning with Flexible Nucleobase Center Representation.bioRxiv : the preprint server for biology · 2023Article
- Challenges and limitations in computational prediction of protein misfolding in neurodegenerative diseases.Frontiers in computational neuroscience · 2023Article
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Motivation: The accuracy gap between predicted and experimental structures has been significantly reduced following the development of AlphaFold2 (AF2). However, for many targets, AF2 models still have room for improvement. In previous CASP experiments, highly computationally intensive MD simulation-based methods have been widely used to improve the accuracy of single 3D models. Here, our ReFOLD pipeline was adapted to refine AF2 predictions while maintaining high model accuracy at a modest computational cost. Furthermore, the AF2 recycling process was utilized to improve 3D models by using them as custom template inputs for tertiary and quaternary structure predictions. Results: According to the Molprobity score, 94% of the generated 3D models by ReFOLD were improved. AF2 recycling showed an improvement rate of 87.5% (using MSAs) and 81.25% (using single sequences) for monomeric AF2 models and 100% (MSA) and 97.8% (single sequence) for monomeric non-AF2 models, as measured by the average change in lDDT. By the same measure, the recycling of multimeric models showed an improvement rate of as much as 80% for AF2-Multimer (AF2M) models and 94% for non-AF2M models. Availability and implementation: Refinement using AlphaFold2-Multimer recycling is available as part of the MultiFOLD docker package (https://hub.docker.com/r/mcguffin/multifold). The ReFOLD server is available at https://www.reading.ac.uk/bioinf/ReFOLD/ and the modified scripts can be downloaded from https://www.reading.ac.uk/bioinf/downloads/. Supplementary information: Supplementary data are available at
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Registered trials
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.