ReviewFrontiers in molecular biosciences2015
Protein flexibility in the light of structural alphabets.
Review in Frontiers in molecular biosciences, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 papers.
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53 citing papers in PubMed.
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- Impact of Ruxolitinib Interactions on JAK2 JH1 Domain Dynamics.International journal of molecular sciences · 2025Article
- Understanding the characteristic behaviour of the wild-type and mutant structure of FLT3 protein by computational methods.Computational and structural biotechnology journal · 2025Article
- A Simple Analysis of the Second (Extra) Disulfide Bridge of VMolecules (Basel, Switzerland) · 2024Article
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- Structure-based pharmacophore modeling and DFT studies of Indian Ocean-derived red algal compounds as PI3Kα inhibitors.Molecular diversity · 2024Article
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- FoldPAthreader: predicting protein folding pathway using a novel folding force field model derived from known protein universe.Genome biology · 2024Article
- The Rapid Evolution of De Novo Proteins in Structure and Complex.Genome biology and evolution · 2024Article
- An In Silico Analysis of Genetic Variants and Structural Modeling of the Human Frataxin Protein in Friedreich's Ataxia.International journal of molecular sciences · 2024Article
- Structural investigation of Trypanosoma cruzi Akt-like kinase as drug target against Chagas disease.Scientific reports · 2024Article
- Evaluation of the Potential Impact of In Silico Humanization on VInternational journal of molecular sciences · 2023Article
- SAFoldNet: A Novel Tool for Discovering and Aligning Three-Dimensional Protein Structures Based on a Neural Network.International journal of molecular sciences · 2023Article
- MDiGest: A Python package for describing allostery from molecular dynamics simulations.The Journal of chemical physics · 2023Article
- Review
- Structural and Dynamic Differences between Calreticulin Mutants Associated with Essential Thrombocythemia.Biomolecules · 2023Article
- General Trends of theInternational journal of molecular sciences · 2023Article
- Discovery of potential FGFR3 inhibitors via QSAR, pharmacophore modeling, virtual screening and molecular docking studies against bladder cancer.Journal of translational medicine · 2023Article
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24 authors.
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Abstract
Protein structures are valuable tools to understand protein function. Nonetheless, proteins are often considered as rigid macromolecules while their structures exhibit specific flexibility, which is essential to complete their functions. Analyses of protein structures and dynamics are often performed with a simplified three-state description, i.e., the classical secondary structures. More precise and complete description of protein backbone conformation can be obtained using libraries of small protein fragments that are able to approximate every part of protein structures. These libraries, called structural alphabets (SAs), have been widely used in structure analysis field, from definition of ligand binding sites to superimposition of protein structures. SAs are also well suited to analyze the dynamics of protein structures. Here, we review innovative approaches that investigate protein flexibility based on SAs description. Coupled to various sources of experimental data (e.g., B-factor) and computational methodology (e.g., Molecular Dynamic simulation), SAs turn out to be powerful tools to analyze protein dynamics, e.g., to examine allosteric mechanisms in large set of structures in complexes, to identify order/disorder transition. SAs were also shown to be quite efficient to predict protein flexibility from amino-acid sequence. Finally, in this review, we exemplify the interest of SAs for studying flexibility with different cases of proteins implicated in pathologies and diseases.
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