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Entropy calculator
Entropy calculator










The Journal of Physical Chemistry Letters 2014, 5 Resolving Internal Motional Correlations to Complete the Conformational Entropy Meter. Iztok Urbančič, Ajasja Ljubetič, and Janez Štrancar.Journal of Chemical Theory and Computation 2016, 12 Computational Methods for Configurational Entropy Using Internal and Cartesian Coordinates. Simon Hikiri, Takashi Yoshidome, and Mitsunori Ikeguchi.Journal of Chemical Theory and Computation 2017, 13 rRNA C-Loops: Mechanical Properties of a Recurrent Structural Motif. Tomáš Dršata, Kamila Réblová, Ivana Beššeová, Jiří Šponer, and Filip Lankaš.The Journal of Physical Chemistry B 2018, 122 An NMR Confirmation for Increased Folded State Entropy Following Loop Truncation. Yulian Gavrilov, Shlomi Dagan, Ziv Reich, Tali Scherf, Yaakov Levy.Journal of Chemical Information and Modeling 2019, 59 How Does the Recently Discovered Peptide MIP Exhibit Much Higher Binding Affinity than an Anticancer Protein p53 for an Oncoprotein MDM2?. Tatsuya Yamada, Tomohiko Hayashi, Simon Hikiri, Naohiro Kobayashi, Hiroshi Yanagawa, Mitsunori Ikeguchi, Masato Katahira, Takashi Nagata, Masahiro Kinoshita.Journal of Chemical Information and Modeling 2020, 60 Entropy of Proteins Using Multiscale Cell Correlation. Arghya Chakravorty, Jonathan Higham, Richard H.Journal of Chemical Theory and Computation 2020, 16 Application and Comprehensive Analysis of Neighbor Approximated Information Theoretic Configurational Entropy Methods to Protein–Ligand Binding Cases. Journal of the American Chemical Society 2021, 143 Quantification of Conformational Entropy Unravels Effect of Disordered Flanking Region in Coupled Folding and Binding. Frederik Friis Theisen, Lasse Staby, Frederik Grønbæk Tidemand, Charlotte O’Shea, Andreas Prestel, Martin Willemoës, Birthe B.This article is cited by 46 publications. The results suggest that in these systems such affinity is achieved by a combination of simultaneously maintaining good protein–ligand contacts while allowing significant residual R/T motion of the ligand through suitable protein motions. Using the BQH method, we then analyze the rotational and translational (R/T) entropy change upon ligand binding for five protein complexes to explore the origins of extremely tight affinity. This method is tested by comparison with the exact Clausius expression for entropy on a range of test molecules ranging from small ligands to a protein. Here we calculate ligand and protein conformational entropies using the Boltzmann–quasiharmonic (BQH) method, which treats the first-order entropy term by the Boltzmann expression for entropy while determining correlations using the quasiharmonic model. While many methods exist to calculate configurational entropy, there is a balance between accuracy and computational demands. Accurate assessment of configurational entropy remains a large challenge in biology.












Entropy calculator