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From nucleotides to numbers: a comprehensive review of RNA feature extraction methods for computational modelling. [PDF]
Brief BioinformSafari F, Tree JJ, Vafaee F.
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Thermodynamic database supports deciphering protein–nucleic acid interactions
Trends in Biotechnology, 2023The thermodynamics of protein-nucleic acid interactions (PNIs) is crucial for elucidating the mechanisms of molecular recognition and pathological consequences. The Protein-Nucleic Acid Thermodynamics Database (PNATDB) is a database containing experimentally determined thermodynamic parameters along with sequence, structural, and function data, which ...
Long-Can Mei, Ge-Fei Hao, Guang-Fu Yang
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Thermodynamics of ligand-nucleic acid interactions.
Methods in enzymology, 1992Ligand-and protein-DNA equilibria are extremely sensitive to solution conditions (e.g., salt, temperature, and pH), and, in general, the effects of different solution variables are interdependent (i.e., linked). As a result, an assessment of the basis for the stability and specificity of ligand-or protein-DNA interactions requires quantitative studies ...
T M, Lohman, D P, Mascotti
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Protein-nucleic acid thermodynamic databases for specific uses.
Trends in biotechnology, 2023In response to Gromiha and Harini, we review the currently available thermodynamic databases for protein-nucleic acid interactions. These databases are designed for particular uses. We give general comments on them to facilitate browsing and exploration.
Long-Can, Mei +2 more
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Quantitative nucleic acids footprinting: thermodynamic and kinetic approaches
Current Opinion in Biotechnology, 1997Quantitative footprinting techniques allow a detailed analysis of the thermodynamic forces that characterize nucleic acid-ligand interactions and ligand-induced changes in nucleic acid structure by separately resolving the intrinsic and cooperative Gibbs free energy changes describing the reactions being investigated.
V, Petri, M, Brenowitz
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Comment on ‘Thermodynamic database supports deciphering protein–nucleic acid interactions’
Trends in Biotechnology, 2023Mei and colleagues reported a thermodynamic database, PNATDB for protein-nucleic acid interactions, which contains 12 635 experimentally determined thermodynamic parameters. They claimed that extracting data from existing databases is difficult. ProNAB, which has more than 20 000 experimental data points for binding affinities of protein-nucleic acid ...
M. Michael Gromiha, Kannan Harini
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Thermodynamics of nucleic acids and their interactions with ligands
Quarterly Reviews of Biophysics, 20001. Introduction 2551.1 General thermodynamics 2562. Nucleic acid thermodynamics 2602.1 DNA duplexes 2612.2 RNA duplexes 2632.3 Hybrid DNA–RNA duplexes 2642.4 Hydration 2672.5 Conformational flexibility 2692.6 Thermodynamics 2723. Nucleic acid–ligand interactions 2773.1 Minor groove binders 2783.2 DNA intercalators 2843.3 Triple-helical systems 2883.3.1
A N, Lane, T C, Jenkins
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Thermodynamic databases for proteins and protein-nucleic acid interactions
Biopolymers, 2001Thermodynamic data regarding proteins and their interactions are important for understanding the mechanisms of protein folding, protein stability, and molecular recognition. Although there are several structural databases available for proteins and their complexes with other molecules, databases for experimental thermodynamic data on protein stability ...
A, Sarai +7 more
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Thermodynamic Characterization of Nucleic Acid Nanoparticles Hybridization by UV Melting
2023The advances in nucleic acid nanotechnology have given rise to various elegantly designed structural complexes fabricated from DNA, RNA, chemically modified RNA strands, and their mixtures. The structural properties of NA nanoparticles (NANP) generally dictate and significantly impact biological function; and thus, it is critical to extract information
Megan, Teter +3 more
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