ArticlePharmaceuticals (Basel, Switzerland)2023
Quality Assessment of Selected Protein Structures Derived from Homology Modeling and AlphaFold.
Article in Pharmaceuticals (Basel, Switzerland), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
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- AI-driven drug-target interaction prediction: current progress, challenges, and future roadmap for precision medicine.Journal of computer-aided molecular design · 2026Review
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- Bioinformatics Approaches for Functional and Structural Annotation and Molecular Docking Study of a Hypothetical Protein From Staphylococcus aureus.BioMed research international · 2026Article
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- Modeling the P2X7 receptor: a comparative analysis of conventional methods and AlphaFold.Frontiers in pharmacology · 2026Article
- Immunoinformatics-based design of a next generation multi-epitope vaccine candidate against Shigella boydii using a hierarchical subtractive proteomics approach.Scientific reports · 2025Article
- Pangenome-Guided Reverse Vaccinology and Immunoinformatics Approach for Rational Design of a Multi-Epitope Subunit Vaccine Candidate Against the Multidrug-Resistant PathogenPharmaceuticals (Basel, Switzerland) · 2025Article
- Dissecting the Dual Drug Candidates Against Glioblastoma and Oligodendroglioma Through Integrated Transcriptome Analysis and Virtual Screening.Cell biochemistry and biophysics · 2025Article
- Novel mutation sites in theJournal of advanced veterinary and animal research · 2025Article
- Interactions of Linalool and Linalyl Acetate with Selected Dog Cytochrome P450 (CYP) Proteins Identified by In Silico Drug Discovery Followed by Molecular Docking Analysis.Pharmaceuticals (Basel, Switzerland) · 2025Article
- Integrated machine learning, molecular dynamics, and DFT-based approach to elucidate the inhibitory effect of Ciprofloxacin analogues against fluoroquinolone-resistant Salmonella Typhi.Archives of microbiology · 2025Article
- FIBOS: R and python packages for analyzing protein packing and structure.Bioinformatics (Oxford, England) · 2025Article
- A robust comprehensive immunoinformatics approach for designing a potential multi-epitope based vaccine against a reiterated monkeypox virus.Biochemistry and biophysics reports · 2025Article
Corrections and comments
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Authors and funding
4 authors.
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Abstract
With technology advancing, many prediction algorithms have been developed to facilitate the modeling of inherently dynamic and flexible macromolecules such as proteins. Improvements in the prediction of protein structures have attracted a great deal of attention due to the advantages they offer, e.g., in drug design. While trusted experimental methods, such as X-ray crystallography, NMR spectroscopy, and electron microscopy, are preferred structure analysis techniques, in silico approaches are also being widely used. Two computational methods, which are on opposite ends of the spectrum with respect to their modus operandi, i.e., homology modeling and AlphaFold, have been established to provide high-quality structures. Here, a comparative study of the quality of structures either predicted by homology modeling or by AlphaFold is presented based on the characteristics determined by experimental studies using structure validation servers to fulfill the purpose. Although AlphaFold is able to predict high-quality structures, high-confidence parts are sometimes observed to be in disagreement with experimental data. On the other hand, while the structures obtained from homology modeling are successful in incorporating all aspects of the experimental structure used as a template, this method may struggle to accurately model a structure in the absence of a suitable template. In general, although both methods produce high-quality models, the criteria by which they are superior to each other are different and thus discussed in detail.
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