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17,191 results

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Page 1
RNA Thermodynamic Structural Entropy.
Garcia-Martin JA, Clote P. Garcia-Martin JA, et al. PLoS One. 2015 Nov 10;10(11):e0137859. doi: 10.1371/journal.pone.0137859. eCollection 2015. PLoS One. 2015. PMID: 26555444 Free PMC article.
An algorithm to compute the derivational entropy for RNA secondary structures had previously been introduced, using stochastic context free grammars (SCFGs). ...Using data from the Rfam database, we determine that both of our thermodynamic methods, which agree in nu …
An algorithm to compute the derivational entropy for RNA secondary structures had previously been introduced, using stochastic …
Entropy at Bio-Nano Interfaces.
Zhu G, Xu Z, Yan LT. Zhu G, et al. Nano Lett. 2020 Aug 12;20(8):5616-5624. doi: 10.1021/acs.nanolett.0c02635. Epub 2020 Jul 24. Nano Lett. 2020. PMID: 32697100 Review.
Entropy, one of the central concepts of thermodynamics, can be a predominant contribution to structural formation and transition. ...Therefore, this review article seeks to provide a conceptual framework demonstrating that entropy can be exploited to shape th
Entropy, one of the central concepts of thermodynamics, can be a predominant contribution to structural formation and transiti
A structural entropy index to analyse local conformations in intrinsically disordered proteins.
Akhila MV, Narwani TJ, Floch A, Maljković M, Bisoo S, Shinada NK, Kranjc A, Gelly JC, Srinivasan N, Mitić N, de Brevern AG. Akhila MV, et al. J Struct Biol. 2020 Apr 1;210(1):107464. doi: 10.1016/j.jsb.2020.107464. Epub 2020 Jan 21. J Struct Biol. 2020. PMID: 31978465 Free article.
While the definition of rigidity is simple with X-ray structures, the notion of flexibility is linked to high experimental B-factors. The definition of disordered regions is more complex as in these same X-ray structures; it is associated to the position of missing …
While the definition of rigidity is simple with X-ray structures, the notion of flexibility is linked to high experimental B-factors. …
A new structural entropy measurement of networks based on the nonextensive statistical mechanics and hub repulsion.
Tan F, Wang B, Wei D. Tan F, et al. Math Biosci Eng. 2021 Oct 26;18(6):9253-9263. doi: 10.3934/mbe.2021455. Math Biosci Eng. 2021. PMID: 34814344 Free article.
The structure properties of complex networks are an open issue. As the most important parameter to describe the structural properties of the complex network, the structure entropy has attracted much attention. ...Because in the irregular network, the d …
The structure properties of complex networks are an open issue. As the most important parameter to describe the structural pro …
Enthalpy-entropy compensation: the role of solvation.
Dragan AI, Read CM, Crane-Robinson C. Dragan AI, et al. Eur Biophys J. 2017 May;46(4):301-308. doi: 10.1007/s00249-016-1182-6. Epub 2016 Oct 28. Eur Biophys J. 2017. PMID: 27796417 Free PMC article. Review.
Structural modifications to interacting systems frequently lead to changes in both the enthalpy (heat) and entropy of the process that compensate each other, so that the Gibbs free energy is little changed: a major barrier to the development of lead compounds in dru
Structural modifications to interacting systems frequently lead to changes in both the enthalpy (heat) and entropy of the proc
Interpretation of HDX Data by Maximum-Entropy Reweighting of Simulated Structural Ensembles.
Bradshaw RT, Marinelli F, Faraldo-Gómez JD, Forrest LR. Bradshaw RT, et al. Biophys J. 2020 Apr 7;118(7):1649-1664. doi: 10.1016/j.bpj.2020.02.005. Epub 2020 Feb 15. Biophys J. 2020. PMID: 32105651 Free PMC article.
The mechanistic interpretation of HDX data, however, is often qualitative and subjective, owing to a lack of quantitative methods to rigorously translate observed deuteration levels into atomistic structural information. To help address this problem, we have developed a me …
The mechanistic interpretation of HDX data, however, is often qualitative and subjective, owing to a lack of quantitative methods to rigorou …
High-Entropy Alloys for Electrocatalysis: Design, Characterization, and Applications.
Zhang Y, Wang D, Wang S. Zhang Y, et al. Small. 2022 Feb;18(7):e2104339. doi: 10.1002/smll.202104339. Epub 2021 Nov 5. Small. 2022. PMID: 34741405 Review.
High-entropy alloys (HEAs) are expected to function well as electrocatalytic materials, owing to their widely adjustable composition and unique physical and chemical properties. ...Moreover, the existing issues and future trends of HEAs are predicted, which will help furth …
High-entropy alloys (HEAs) are expected to function well as electrocatalytic materials, owing to their widely adjustable composition …
Principles of protein structural ensemble determination.
Bonomi M, Heller GT, Camilloni C, Vendruscolo M. Bonomi M, et al. Curr Opin Struct Biol. 2017 Feb;42:106-116. doi: 10.1016/j.sbi.2016.12.004. Epub 2017 Jan 5. Curr Opin Struct Biol. 2017. PMID: 28063280 Review.
Here, we describe how the well-established principles of protein structure determination should be extended to the case of protein structural ensembles determination. ...We first review the growing literature of recent methods that combine experimental and computati …
Here, we describe how the well-established principles of protein structure determination should be extended to the case of protein …
Conformational entropy in molecular recognition of intrinsically disordered proteins.
Skriver K, Theisen FF, Kragelund BB. Skriver K, et al. Curr Opin Struct Biol. 2023 Dec;83:102697. doi: 10.1016/j.sbi.2023.102697. Epub 2023 Sep 14. Curr Opin Struct Biol. 2023. PMID: 37716093 Free article. Review.
Although methodologically challenging and understudied, emerging studies into their changes in conformational entropy (deltaS(conf)) upon complex formation have provided both quantitative and qualitative insight. ...
Although methodologically challenging and understudied, emerging studies into their changes in conformational entropy (deltaS(conf)) …
Microsecond MD Simulations of the Plexin-B1 RBD: N-H Probability Density as Descriptor of Structural Dynamics, Dimerization-Related Conformational Entropy, and Transient Dimer Asymmetry.
Pshetitsky Y, Mendelman N, Li Z, Zerbetto M, Buck M, Meirovitch E. Pshetitsky Y, et al. J Phys Chem B. 2022 Sep 1;126(34):6396-6407. doi: 10.1021/acs.jpcb.2c03431. Epub 2022 Aug 18. J Phys Chem B. 2022. PMID: 35980340
The L1 and L3 loops are throughout highly flexible, the L2 loop and the secondary structure elements are generally rigid, and the L4 loop is flexible in the monomer and rigid in the dimer. ...In summary, bond-vector P(eq) functions derived directly from long MD simulations …
The L1 and L3 loops are throughout highly flexible, the L2 loop and the secondary structure elements are generally rigid, and the L4 …
17,191 results
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