ArticleBMC bioinformatics2023
Role of environmental specificity in CASP results.
Article in BMC bioinformatics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- The Shape of Things to Come: α-Helical Membrane Protein Folding on the Ribosome.Chemical reviews · 2026Review
- Heat Shock Protein and Disaggregase Influencing the Casein Structuralisation.International journal of molecular sciences · 2025Article
- Chameleon sequences-Structural effects.PloS one · 2025Article
- Protein folding: Funnel model revised.Computational and structural biotechnology journal · 2024Article
- The hemostatic activity and Mechanistic roles of glucosyloxybenzyl 2-isobutylmalate extract (BSCE) fromHeliyon · 2024Article
- Chameleon Sequences-Structural Effects in Proteins Characterized by Hydrophobicity Disorder.ACS omega · 2024Article
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Authors and funding
3 authors.
Funding
Abstract
backgroundRecently, significant progress has been made in the field of protein structure prediction by the application of artificial intelligence techniques, as shown by the results of the CASP13 and CASP14 (Critical Assessment of Structure Prediction) competition. However, the question of the mechanism behind the protein folding process itself remains unanswered. Correctly predicting the structure also does not solve the problem of, for example, amyloid proteins, where a polypeptide chain with an unaltered sequence adopts a different 3D structure.
resultsThis work was an attempt at explaining the structural variation by considering the contribution of the environment to protein structuring. The application of the fuzzy oil drop (FOD) model to assess the validity of the selected models provided in the CASP13, CASP14 and CASP15 projects reveals the need for an environmental factor to determine the 3D structure of proteins. Consideration of the external force field in the form of polar water (Fuzzy Oil Drop) and a version modified by the presence of the hydrophobic compounds, FOD-M (FOD-Modified) reveals that the protein folding process is environmentally dependent. An analysis of selected models from the CASP competitions indicates the need for structure prediction as dependent on the consideration of the protein folding environment.
conclusionsThe conditions governed by the environment direct the protein folding process occurring in a certain environment. Therefore, the variation of the external force field should be taken into account in the models used in protein structure prediction.
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