11. Accurate estimation of the entropy of rotation-translation probability distributionsFederico 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.
Ključne besede: entropy, probability distribution, molecular dynamics, nearest-neighbor
Objavljeno v RUNG: 11.10.2016; Ogledov: 4387; Prenosov: 0
Gradivo ima več datotek! Več... |
12. Molecular dynamics simulations and docking enable to explore the biophysical factors controlling the yields of engineered nanobodiesMiguel Soler, Ario De Marco, Sara Fortuna, 2016, izvirni znanstveni članek Opis: Nanobodies (VHHs) have proved to be valuable substitutes of conventional antibodies for molecular
recognition. Their small size represents a precious advantage for rational mutagenesis based on
modelling. Here we address the problem of predicting how Camelidae nanobody sequences can tolerate
mutations by developing a simulation protocol based on all-atom molecular dynamics and wholemolecule
docking. The method was tested on two sets of nanobodies characterized experimentally
for their biophysical features. One set contained point mutations introduced to humanize a wild type
sequence, in the second the CDRs were swapped between single-domain frameworks with Camelidae
and human hallmarks. The method resulted in accurate scoring approaches to predict experimental
yields and enabled to identify the structural modifications induced by mutations. This work is a
promising tool for the in silico development of single-domain antibodies and opens the opportunity to
customize single functional domains of larger macromolecules
Ključne besede: nanobodies, molecular dynamics, modeling, antibody solubility
Objavljeno v RUNG: 11.10.2016; Ogledov: 4689; Prenosov: 244
 Celotno besedilo (1,95 MB) |
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14. Evaluation of commercially available ferrites for solar hydrogen production by two-step water splitting thermochemical cyclesFernando Fresno, Rocío Fernández-Saavedra, M. Belén Gómez-Mancebo, Miguel Sánchez, M. Isabel Rucandio, Alberto J. Quejido, Manuel Romero, 2008, objavljeni povzetek znanstvenega prispevka na konferenci Ključne besede: železo, vodik, sončna energija, termokemični cikli
Objavljeno v RUNG: 15.10.2013; Ogledov: 7270; Prenosov: 38
 Povezava na celotno besedilo |
