entropy

..Our method appears superior when compared to other bioinformatics approaches, such as the evolutionary trace method, entropy-variability plot, and correlated mutation analysis, both qualitatively and quantitatively.

We use approximate entropy and hydrophobicity patterns to predict G-protein-coupled receptors. Adaboost classifier is adopted as the prediction engine. A low homology dataset is used to validate the proposed method...

..Despite much recent interest in quantification of heart rate variability (HRV), the prognostic value of conventional measures of HRV and of newer indices based on nonlinear dynamics is not universally accepted...

..Historically it has been virtually impossible to experimentally estimate changes in protein conformational entropy, a potentially important component of the free energy of protein association...

..This leads to smaller energy differences between different geometries and helps explain the extreme structural polymorphism of the human telomeric G-quadruplexes...

..More recently transfer entropy, an information-theoretic measure of time-directed information transfer between jointly dependent processes, has ..

Recognition of pathogens relies on families of proteins showing great diversity. Here we construct maximum entropy models of the sequence repertoire, building on recent experiments that provide a nearly exhaustive sampling of the IgM ..

..Similar effects could potentially be exploited in nuclear receptor drug design...

The concept of entropy is described and its characteristics discussed as applied in tissue-based diagnosis. The concept of entropy includes at least 2 points of view--thermodynamic and informatics perspectives...

..We also found that the entropy production of the whole network, characterizing the dissipation costs from the combined effects of both ..

..One of the important goals of microarray research is the identification of genes whose expression is considerably higher or lower in some tissues than in others. We would like to have ways of identifying such tissue-specific genes...

..Purely cognitive feedback apparently engages the same regions as rewarding stimuli, consistent with a broader characterization of this network...

..These maximum entropy models are equivalent to Ising models, and predict that larger networks are completely dominated by correlation ..

..The approach relies on: 1) the calculation of Shannon entropy (SE) of the distribution of patterns lasting three beats; 2) the calculation of a regularity index based on an ..

Approximate entropy (ApEn) measures regularity in time series data, while traditional linear statistics measure variability...

..rate of new patterns along a digital sequence, is closely related to such important source properties as entropy and compression ratio, but, in contrast to these, it is a property of individual sequences...

..This age-related increase in cellular entropy is compatible with the disposable soma theory of aging...

Sequence entropy-variability plots based on alignments of very large numbers of sequences-can indicate the location in proteins of the main active site and modulator sites...

..Here we propose to use the image texture entropy as an objective measurement that reflects the structural deterioration of the C...

We propose to estimate transfer entropy using a technique of symbolization...

..As an example, we consider exponentially distributed inputs, which are known to approximate a variety of signals from natural environment...

..Approximate entropy (ApEn), a regularity statistic from nonlinear dynamics, recently has demonstrated relatively good measurement ..

..pattern discovery (Bipad), which produces a mathematical model based on information maximization or Shannon's entropy minimization principle, for discovery of bipartite sequence patterns...

..Because nonlinear methods of HRV analysis provide information about heart rate dynamics not evident from usual HRV measures, we also hypothesized that approximate entropy (ApEn), a nonlinear measure of HRV, might have predictive value.

..Being considerably more flexible, type II conformers are stabilized by entropy and the relative abundances of two conformers of this type (IIb(2) and IIc(1)) are shown to significantly ..

..such obstacles: crystallization using carrier proteins or antibody complexes, chemical modification, surface entropy reduction, proteolytic digestion, and additive screening...

..Transfer entropy (TE) is an alternative measure of effective connectivity based on information theory...

..as a result of entropic forces, despite their strong confinement within the cell; in other words, we propose that entropy can act as a primordial physical force which drives chromosome segregation under the right physical conditions...

..Despite the fundamental importance of both enthalpy and entropy in driving ligand binding, the role of conformational entropy is rarely addressed in drug design...

The restriction of a small molecule's motion on binding to a protein causes a loss of configurational entropy, and thus a penalty in binding affinity...

..We quantified COP dynamics in terms of sample entropy (regularity), standard deviation (variability), sway-path length of the normalized posturogram (curviness), ..

This paper presents an analysis of entropy-based molecular descriptors...

..The method is based on the definition of an uncoupling function calculating, by means of entropy rates, the minimum amount of independent information (i.e...

..The data best support the conclusion that the mechanistic strategy of RecA likely relies on intrinsic DNA dynamics...

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..This study aimed at making use of a novel approach based on entropy to select suitable genomic regions from which to infer the phylogeny of papillomavirus...

..The N-terminal deletion of rbetaA3 (rbetaA3Ntr) significantly increases the enthalpy (+10.9 kcal/mol) and entropy (+40.7 cal/deg mol) of binding relative to unmodified protein...

..In this study, we demonstrated the use of two distinct methods of image texture analysis, the Shannon's entropy [standard error (SE)], and the fractal dimension (FD) to characterize the formation and remodeling of newly ..

..Two different methods were used to estimate the regularity of the EEG background activity: spectral entropy (SpecEn) and sample entropy (SampEn)...

..An explicit computational model of structural adaptation and computation of the quasiharmonic entropy of association were obtained from the MD...

Conformational entropy makes important contribution to the stability and folding of RNA molecule, but it is challenging to either measure or compute conformational entropy associated with long loops...

..Our approach addresses several significant challenges that accompany the study of junction folding, and should prove useful in defining the thermodynamic determinants of stability in these important RNA motifs...

..This paper proposes a neural-network-based automated epileptic EEG detection system that uses approximate entropy (ApEn) as the input feature...

Sample Entropy (SampEn) has been proposed as a method to overcome limitations associated with approximate entropy (ApEn)...

..In order to improve the accuracy of GRNs inference methods based on entropy (mutual information), a new criterion function is here proposed.

..These results support the hypothesized relationship between basal ganglia and visuomotor sequential learning, but demonstrate the importance of context upon sequence learning...

..visual) and bimodal (combined auditory and visual) stimuli were analyzed by applying a new method called wavelet entropy (WE)...

..the (effective) energy of interaction, reorganization energy of the ligand and the macromolecule, conformational entropy change of the ligand and the macromolecule, and translational and rotational entropy loss of the ligand...

..These results highlight the importance of hydrogen bonding interactions during primer extension and pyrophosphorolysis...

..The sample entropy was higher in the schizophrenic patients compared to controls in the time series from the activity counts made ..

..The repacked conformations have native packing density as measured by a standard Voronoi procedure. Entropy is distributed non-uniformly over positions, and we partially explain the observed distribution using rotamer ..

Multiscale entropy (MSE) is a recently proposed entropy-based index of physiological complexity, evaluating signals at multiple temporal scales...

..In silico evolution provides a quantitative demonstration that continuous positive selection can generate complex phenotypes from simple components by incremental evolution, as Darwin proposed...

..A systematic study of a large set of NMR-determined proteins is analyzed using a novel method based on entropy maximization to demonstrate that the next level of refinement in the elastic network model description of ..

The largest force disfavoring the folding of a protein is the loss of conformational entropy. A large contribution to this entropy loss is due to the side-chains, which are restricted, although not immobilized, in the folded protein...

..Ideally, this method should not require a pre-specified model of the interaction. Transfer entropy--an information theoretic implementation of Wiener-type causality--is a method for the investigation of causal ..

..to quantify methylation difference and identify DMRs from genome-wide methylation profiles by adapting Shannon entropy. QDMR was applied to synthetic methylation patterns and methylation profiles detected by methylated DNA ..

Amino acid background distribution is an important factor for entropy-based methods which extract sequence conservation information from protein multiple sequence alignments (MSAs)...

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..K d data yielded an unfavorable enthalpy change, Delta H degrees = 14 +/- 3 kcal/mol, offset by a favorable entropy term, TDelta S degrees = 23 +/- 3 kcal/mol...

..In this study, sample entropy (SampEn) was investigated as a measure of complexity using a dog model...

..In statistical physics, a method of inference based on information entropy results in a complete macro-scale description of classical thermodynamic systems in terms of the state variables ..

..core element of the two AT-hooks, which penetrates deep into the minor groove, is entropically driven: both the entropy and enthalpy of association of the peptides to the target DNA are positive up to 50 degrees C...

..A decline in the quality of recently deposited A. phagocytophilum sequences was also demonstrated...

..literatures, the relationship between the four subtests of the Culture-Fair Intelligence Test (CFIT) and the entropy of the Ruiz Absolute Scale of Complexity Management (R-ASCM) was investigated...

..The current may reverse its direction several times when temperature or the phase shift is changed. The authors' model is to describe the movement of molecular motors along microtubule...

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..In the present algorithm, free energy calculations proceed by the realization of an energy difference space random walk. Thereby, this algorithm can greatly improve the sampling of the regions in phase space where target states overlap...

..Analytic results and preliminary thermochemical tests indicate that our model also improves upon the simple, local-density-based exchange hole model of Iikura et al. [J. Chem. Phys. 115, 3540 (2001)]...

..The changes of the kinetics that occur upon changing the parameters of the underlying binding-folding energy landscape are studied...

..The strong ideality of urea solutions in some concentration scales (incidentally implying a lack of water perturbation) is discussed in terms of recent data and ideas on the mechanism of urea denaturation of proteins...

..mechanic and thermodynamic approaches allow us to count states in an approximate manner to quantify the entropy and energy of the energy landscape within a folding funnel for an alpha-helical protein...

We have developed a novel method to compute the conformational entropy of any molecular system via conventional simulation techniques...

..These could enable us to identify the downhill folding or the cooperative two-state folding behavior solely from the native structures of proteins...

..The procedure is illustrated with the model system of the phosphotyrosine peptide binding to the Src SH2 domain...

..It is applied to a simple model system focusing on the translational entropy of the solvent...

..The effects of electrostatics on cluster speciation and morphology are discussed based on results from a set of simulations carried out with the ionic charges removed...

..Gibbs introduced the quantity s(rho)=-integralrho log rho dmu as an analog of the thermodynamical entropy. Attempts to reach a closer analogy between thermodynamical and Gibbs entropy lead to the idea to modify the last ..

..Our analysis is quantitatively consistent with the available thermodynamic and kinetic data on slow two-state folding proteins and provides a straightforward explanation for the apparent fast-folding paradox...

..The effect of a variety of factors, including the pore size and the proteins' length, as well as the temperature, is studied in detail...

..Finally, we show that all the formulations of the fluctuation theorem can be understood from the notion of entropy production.

..as global minima of their effective potential energy surfaces, which largely neglected the conformational entropy because decoys composed of only lowest-energy conformations were used to optimize the force field...

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Solvent entropy change is a major factor in driving the association of hydrophobic species in aqueous solutions. We have developed a novel methodology which simulates the solvation of hydrophobic surfaces by water...

..Experimental measurements of slaving of myoglobin motions indicate that a major fraction of functionally important motions have significant entropic barriers...

..This provides important insight into the molecular mechanism of effector-mediated derepression...

..native state has a funnel shape and that the free energy barrier to folding arises from the chain configurational entropy only...

..The barrier to folding is the formation of predominantly local structures such as helices and hairpins, which are needed to bring nonlocal pairs of amino acids into contact...

..The nature of activating the various steps in the binding process seems to be one overall involving substantial entropic changes...

..Catalytic effect of engineered disulfide bridges was rationalized by characterizing the concerted motions of the two domains...

..We have also calculated the entropy and effective energy for the different states along the unfolding pathway and found that the tetramerization is ..

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..The activation enthalpy and entropy for unfolding do not depend noticeably on temperature and are both significantly greater than those for the ..

..5 compared with pH 6.8. This decrease could be attributed to a weaker binding of the C terminus of stathmin. These findings do not support the view that stathmin works as a pH-sensitive protein...

..e., covalent bonds, salt-bridges, hydrogen-bonds, and torsional-forces, each associated with an enthalpy and entropy contribution...

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..The implications of these results are discussed in the context of estimates for the backbone entropy of single residues, and for the ability of all-atom simulations to reproduce experimental protein folding data.

..Our results confirm and quantify the hypothesis, recently formulated on the basis of experimental data, that the folding landscape of protein S6 is strongly affected by an atypical distribution of contact energies...

..We find that entropic excluded volume effects are crucially important for stabilizing the organized native state relative to the molten globule...

..This reveals that loading influences the process via the activation entropy, not energy. No prior clinical trial of a heating device or strategy has accounted for this coupling...

..of cortical somatosensory evoked potentials (SSEP) will track recovery of normal thalamocortical coupling, and c) entropy-based quantitative EEG (qEEG) analysis will capture sequential changes in thalamocortical coupling during ..

..density-overcoming energetic penalties due to electrostatics repulsion, DNA bending stiffness, and entropy. Because this motor is comprised of a pentameric ring of ASCE ATPases, its study will shed important light into ..

..interact with? For example, do residues contacting portions of a ligand expected to have high configurational entropy (such as the valeric acid tails of biotin) have a different energetic challenge than those residues contacting ..

..As well as the mean thermodynamic properties enthalpy and entropy, fluctuation properties such as heat capacity and compressibility are useful for understanding contributions to ..

..transertion (the coupling of transcription and co-translational insertion of proteins into the membrane], and entropy. And the role of the recently discovered MreB cytoskeleton remains unclear...

..transertion (the coupling of transcription and co-translational insertion of proteins into the membrane], and entropy. And the role of the recently discovered MreB cytoskeleton remains unclear...

..transertion (the coupling of transcription and co-translational insertion of proteins into the membrane], and entropy. And the role of the recently discovered MreB cytoskeleton remains unclear...

..The second question is whether the entropy change that contributes to the action of an allosteric ligand is related to changes in enzyme dynamics...

..The second question is whether the entropy change that contributes to the action of an allosteric ligand is related to changes in enzyme dynamics...

..Temporal instability and spatial variance will be measured using spatial correlation analysis and global entropy. Spatiotemporal analysis of high-speed imaging data will be further applied to study vibratory characteristics of ..

..Temporal instability and spatial variance will be measured using spatial correlation analysis and global entropy. Spatiotemporal analysis of high-speed imaging data will be further applied to study vibratory characteristics of ..

..Temporal instability and spatial variance will be measured using spatial correlation analysis and global entropy. Spatiotemporal analysis of high-speed imaging data will be further applied to study vibratory characteristics of ..

..pentapeptides of Met- enkephalin and Leu-enkephalin in the presence of water, (iii) calculations of the relative entropy and relative free energy, and (iv) constrained peptide systems...

..of the extent to which the enzyme catalyzes the reaction by lowering the enthalpy and/or by raising the entropy of activation...

..of VLPO cause resistance to anesthetic hypnosis as determined by righting reflex assays and processed EEG entropy. Finally, we will determine if light-induced depolarization of VLPO causes hypersensitivity to anesthetic ..

..density--overcoming energetic penalties due to electrostatic repulsion, DNA bending stiffness, and entropy. A single molecule optical tweezers assay has enabled real time measurement of phage phi29 packaging and shows ..

..interactions, by using equilibrium dialysis in Hummel-Dreyer chromatography to measure free energy, enthalpy, and entropy of binding of putrescine, spermidine, spermine, and analogs of these as functions of ionic strength. 2...

..calorimetry (ITC), a powerful method that provides a thorough thermodynamic profile for binding (enthalpy, entropy, free energy, and dissociation constants)...

..calorimetry (ITC), a powerful method that provides a thorough thermodynamic profile for binding (enthalpy, entropy, free energy, and dissociation constants)...