ArticleNucleic acids research2017
ReFOLD: a server for the refinement of 3D protein models guided by accurate quality estimates.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Protein Structure Prediction Methods.Advances in experimental medicine and biology · 2026Review
- Prediction of protein structures, functions and interactions using the IntFOLD7, MultiFOLD and ModFOLDdock servers.Nucleic acids research · 2023Article
- Comparative genomics and interactomics of polyadenylation factors for the prediction of new parasite targets: Entamoeba histolytica as a working model.Bioscience reports · 2023Article
- Improvement of protein tertiary and quaternary structure predictions using the ReFOLD refinement method and the AlphaFold2 recycling process.Bioinformatics advances · 2023Article
- Proteomic Tools for the Analysis of Cytoskeleton Proteins.Methods in molecular biology (Clifton, N.J.) · 2022Article
- A Systematic Immuno-Informatic Approach to Design a Multiepitope-Based Vaccine Against Emerging Multiple Drug ResistantFrontiers in immunology · 2022Article
- A NovelBiology · 2021Article
- Molecular Analysis of Streptomycin Resistance Genes in Clinical Strains ofAntibiotics (Basel, Switzerland) · 2021Article
- Fast and effective protein model refinement using deep graph neural networks.Nature computational science · 2021Article
- Antibacterial effects assessment on some livestock pathogens, thermal stability and proposing a probable reason for different levels of activity of thanatin.Scientific reports · 2021Article
- Computational Methods for the Elucidation of Protein Structure and Interactions.Methods in molecular biology (Clifton, N.J.) · 2021Review
- Article
- IntFOLD: an integrated web resource for high performance protein structure and function prediction.Nucleic acids research · 2019Article
- Methods for the Refinement of Protein Structure 3D Models.International journal of molecular sciences · 2019Review
- Modeling the Tertiary Structure of the Rift Valley Fever Virus L Protein.Molecules (Basel, Switzerland) · 2019Article
- Predictive and Experimental Approaches for Elucidating Protein-Protein Interactions and Quaternary Structures.International journal of molecular sciences · 2017Review
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
ReFOLD is a novel hybrid refinement server with integrated high performance global and local Accuracy Self Estimates (ASEs). The server attempts to identify and to fix likely errors in user supplied 3D models of proteins via successive rounds of refinement. The server is unique in providing output for multiple alternative refined models in a way that allows users to quickly visualize the key residue locations, which are likely to have been improved. This is important, as global refinement of a full chain model may not always be possible, whereas local regions, or individual domains, can often be much improved. Thus, users may easily compare the specific regions of the alternative refined models in which they are most interested e.g. key interaction sites or domains. ReFOLD was used to generate hundreds of alternative refined models for the CASP12 experiment, boosting our group's performance in the main tertiary structure prediction category. Our successful refinement of initial server models combined with our built-in ASEs were instrumental to our second place ranking on Template Based Modeling (TBM) and Free Modeling (FM)/TBM targets. The ReFOLD server is freely available at: http://www.reading.ac.uk/bioinf/ReFOLD/.
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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.