ArticleNucleic acids research2019
GalaxyRefine2: simultaneous refinement of inaccurate local regions and overall protein structure.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 66 papers.
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Who cites it
66 citing papers in PubMed.
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- PROPTIMUS LIVE: local constrained α-carbon optimization of proteins.Nucleic acids research · 2026Article
- A mutation-aware proteomics approach for designing a multi-epitope vaccine against multidrug-resistantMicrobiology spectrum · 2026Article
- In silico design and immunoinformatics evaluation of a multi-epitope vaccine targeting SEPT9 for gastrointestinal adenocarcinomas.BMC immunology · 2026Article
- Immunoinformatics-driven design of a conserved RNA-dependent RNA polymerase-based multi-epitope vaccine against avian infectious bronchitis virus.Veterinary world · 2026Article
- A multi-epitope pan-betacoronavirus vaccine construct predicted to induce broad-spectrum and durable immune responses: an immunoinformatics approach.Frontiers in bioinformatics · 2026Article
- From computational screening toFrontiers in microbiology · 2026Article
- Design and in silico evaluation of an mRNA vaccine against HTLV-1 using AI-driven reverse vaccinology approaches.PloS one · 2026Article
- A Comprehensive Review on Homology Modelling in Drug Development: Methodologies, Tools, and Evaluation.Mini reviews in medicinal chemistry · 2026Review
- Integrative in vitro and in silico evaluation of HSP60-derived peptides as immunomodulators of the TLR4/MD-2 complex.Scientific reports · 2025Article
- PIK3R1 as the Hidden Hand in Arrhythmogenic Right Ventricular Cardiomyopathy Inflammation: Weaving Transcriptomic Signatures with Structural Therapeutic Insights.Pharmaceuticals (Basel, Switzerland) · 2025Article
- Computational Development of Multi-Epitope Reovirus Vaccine with Potent Predicted Binding to TLR2 and TLR4.Pharmaceuticals (Basel, Switzerland) · 2025Article
- An integrated structural and immunoinformatic approach to design a multi-epitope based vaccine against the foot-and-mouth disease virus.Scientific reports · 2025Article
- An immunoinformatics-based designed multi-epitope candidate vaccine against Mycoplasma pneumoniae.BMC microbiology · 2025Article
- Structure-guided design of a novel, stable, and soluble Cecropin A variant for antimicrobial therapeutic applications.Scientific reports · 2025Article
- Targeting Streptococcus pyogenes atpF protein for multi-epitope vaccine development: a genomics-driven immunoinformatics strategy.Journal, genetic engineering & biotechnology · 2025Article
- Design of a novel multiepitope vaccine against glioblastoma by in silico approaches.Scientific reports · 2025Article
- Immunoinformatics-Based development of a Multi-Epitope vaccine candidate targeting coinfection by Klebsiella pneumoniae and Acinetobacter baumannii.BMC infectious diseases · 2025Article
6 more citing papers are in PubMed but not listed here.
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4 authors.
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Abstract
The 3D structure of a protein can be predicted from its amino acid sequence with high accuracy for a large fraction of cases because of the availability of large quantities of experimental data and the advance of computational algorithms. Recently, deep learning methods exploiting the coevolution information obtained by comparing related protein sequences have been successfully used to generate highly accurate model structures even in the absence of template structure information. However, structures predicted based on either template structures or related sequences require further improvement in regions for which information is missing. Refining a predicted protein structure with insufficient information on certain regions is critical because these regions may be connected to functional specificity that is not conserved among related proteins. The GalaxyRefine2 web server, freely available via http://galaxy.seoklab.org/refine2, is an upgraded version of the GalaxyRefine protein structure refinement server and reflects recent developments successfully tested through CASP blind prediction experiments. This method adopts an iterative optimization approach involving various structure move sets to refine both local and global structures. The estimation of local error and hybridization of available homolog structures are also employed for effective conformation search.
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