ArticleProtein science : a publication of the Protein Society2017
Homology modeling in a dynamical world.
Article in Protein science : a publication of the Protein Society, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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8 citing papers in PubMed, 26 citations in OpenAlex.
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- Molecular Modelling in Bioactive Peptide Discovery and Characterisation.Biomolecules · 2025Review
- Making Use of Averaging Methods in MODELLER for Protein Structure Prediction.International journal of molecular sciences · 2024Article
- Insights Into The Effects of Amino Acid Substitutions on The Stability of Reteplase Structure: A Molecular Dynamics Simulation Study.Iranian journal of biotechnology · 2023Article
- Easy Not Easy: Comparative Modeling with High-Sequence Identity Templates.Methods in molecular biology (Clifton, N.J.) · 2023Article
- What the protein data bank tells us about the evolutionary conservation of protein conformational diversity.Protein science : a publication of the Protein Society · 2022Article
- ModFlex: Towards Function Focused Protein Modeling.Journal of molecular biology · 2021Article
- Bioinformatic analysis of subfamily-specific regions in 3D-structures of homologs to study functional diversity and conformational plasticity in protein superfamilies.Computational and structural biotechnology journal · 2021Article
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4 authors at 2 institutions in 1 country.
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Abstract
A key concept in template-based modeling (TBM) is the high correlation between sequence and structural divergence, with the practical consequence that homologous proteins that are similar at the sequence level will also be similar at the structural level. However, conformational diversity of the native state will reduce the correlation between structural and sequence divergence, because structural variation can appear without sequence diversity. In this work, we explore the impact that conformational diversity has on the relationship between structural and sequence divergence. We find that the extent of conformational diversity can be as high as the maximum structural divergence among families. Also, as expected, conformational diversity impairs the well-established correlation between sequence and structural divergence, which is nosier than previously suggested. However, we found that this noise can be resolved using a priori information coming from the structure-function relationship. We show that protein families with low conformational diversity show a well-correlated relationship between sequence and structural divergence, which is severely reduced in proteins with larger conformational diversity. This lack of correlation could impair TBM results in highly dynamical proteins. Finally, we also find that the presence of order/disorder can provide useful beforehand information for better TBM performance.
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