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Experimental indicators of ergonomic wellness and quality of life
Tanja Peric, A. Comin, M. Montillo, A. Prandi, P. L. Esposito, M. Mascolo, G. Tubaro, 2012, izvirni znanstveni članek

Najdeno v: osebi
Ključne besede: lasje, slina, kortizol, ergonomija
Objavljeno: 16.06.2016; Ogledov: 1811; Prenosov: 119
URL Polno besedilo (0,00 KB)

Distance-based configurational entropy of proteins from molecular dynamics simulations
Federico Fogolari, Alessandra Corazza, Sara Fortuna, Miguel Angel Soler, Bryan VanSchouwen, Giorgia Brancolini, Stefano Corni, Giuseppe Melacini, Gennaro Esposito, 2015, izvirni znanstveni članek

Opis: Estimation of configurational entropy from molecular dynamics trajectories is a difficult task which is often performed using quasi-harmonic or histogram analysis. An entirely different approach, proposed recently, estimates local density distribution around each conformational sample by measuring the distance from its nearest neighbors. In this work we show this theoretically well grounded the method can be easily applied to estimate the entropy from conformational sampling. We consider a set of systems that are representative of important biomolecular processes. In particular: reference entropies for amino acids in unfolded proteins are obtained from a database of residues not participating in secondary structure elements; the conformational entropy of folding of β2-microglobulin is computed from molecular dynamics simulations using reference entropies for the unfolded state; backbone conformational entropy is computed from molecular dynamics simulations of four different states of the EPAC protein and compared with order parameters (often used as a measure of entropy); the conformational and rototranslational entropy of binding is computed from simulations of 20 tripeptides bound to the peptide binding protein OppA and of β2-microglobulin bound to a citrate coated gold surface. This work shows the potential of the method in the most representative biological processes involving proteins, and provides a valuable alternative, principally in the shown cases, where other approaches are problematic.
Najdeno v: osebi
Ključne besede: entropy, protein, molecular dynamics, simulations, MD
Objavljeno: 12.10.2016; Ogledov: 1840; Prenosov: 150
.pdf Polno besedilo (2,40 MB)

Accurate estimation of the entropy of rotation-translation probability distributions
Federico Fogolari, Cedrix Jurgal Dongmo Foumthuim, Sara Fortuna, Miguel Angel Soler, Alessandra Corazza, Gennaro Esposito, 2016, izvirni znanstveni članek

Opis: The estimation of rotational and translational entropies in the context of ligand binding has been the subject of long-time investigations. The high dimensionality (six) of the problem and the limited amount of sampling often prevent the required resolution to provide accurate estimates by the histogram method. Recently, the nearest-neighbor distance method has been applied to the problem, but the solutions provided either address rotation and translation separately, therefore lacking correlations, or use a heuristic approach. Here we address rotational–translational entropy estimation in the context of nearest-neighbor-based entropy estimation, solve the problem numerically, and provide an exact and an approximate method to estimate the full rotational–translational entropy.
Najdeno v: osebi
Ključne besede: entropy, probability distribution, molecular dynamics, nearest-neighbor
Objavljeno: 11.10.2016; Ogledov: 1885; Prenosov: 0
.pdf Polno besedilo (1,47 MB)

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