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The influence of n-linked glycans on the molecular dynamics of the hiv-1 gp120 v3 loop
(Public Library of Science (PLoS), 2013-11-26)
N-linked glycans attached to specific amino acids of the gp120 envelope trimer of a HIV virion can modulate the binding affinity of gp120 to CD4, influence coreceptor tropism, and play an important role in neutralising ...
Molecular simulations of carbohydrates and protein–carbohydrate interactions: motivation, issues and prospects
(Elsevier BV, 2010-08-01)
The characterization of the 3D structure of oligosaccharides, their conjugates and analogs is particularly challenging for traditional experimental methods. Molecular simulation methods provide a basis for interpreting ...
On the role of water models in quantifying the binding free energy of highly conserved water molecules in proteins: the case of concanavalin a
(American Chemical Society (ACS), 2011-10-11)
The ability of ligands to displace conserved water molecules in protein binding sites is of significant interest in drug design and is particularly pertinent in the case of glycomimetic drugs. This concept was explored in ...
Contribution of the empirical dispersion correction on the conformation of short alanine peptides obtained by gas-phase qm calculations
(Canadian Science Publishing, 2013-09-01)
In this work we analyze the effect of the inclusion of an empirical dispersion term to standard DFT (DFT-D) in the prediction of the conformational energy of the alanine dipeptide (Ala2) and in assessing the relative ...