Summary A graphical user interface for the GROMACS program has been developed as plugins for YASARA molecular graphics suite. The most significant GROMACS methods can be run entirely via a windowed menu system, and the results are shown on screen in real-time. Availability and Implementation YAMACS is written in Python and is freely available for download at https://github.com/YAMACS-SML/YAMACS and is supported on Linux. It has been released under GPL-3.0 license. Supplementary information YAMACS User Manual, available at https://github.com/YAMACS-SML/YAMACS

Sphingolipids are a class of lipids acting as key modulators of many physiological and pathophysiological processes. Hydroxylation patterns have a major influence on the biophysical properties of sphingolipids. In this work, we have studied the mechanism of action of hydroxylated lipids in sphingomyelin synthase (SMS). The structures of the two human isoforms, SMS1 and SMS2, have been generated through neural network supported homology. Furthermore, we have elucidated the reaction mechanism that allows SMS to recover the choline head from a phosphocholine (PC) and transfer it to ceramide, and we have clarified the role of the hydroxyl group in the interaction with the enzyme. Finally, the effect of partial inhibition of SMS on the levels of PC and sphingomyelin was calculated for different rate constants solving ordinary differential equation systems.

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The study of ligand-receptor interactions through computational techniques, such as molecular dynamics (MD) and docking, has several limitations due to their temporal and spatial dimensions. Docking can reasonably identify the pose and energy of interaction but cannot distinguish between agonist and antagonist. MD allows us to collect useful information on the thermodynamics and kinetics of the whole system but a method is needed to extract information on receptor activity. In this work, we extracted the dihedral angles of the receptor backbone and the RMSD of each residue during a dynamic of 20 ns. We used Sysa coding to reduce the information of the entire receptor system to a collection of strings, one for each snapshot of the dynamics. The strings are compared with an alignment-free approach and a distance calculated for each one. The comparison of distances makes it possible to discriminate against the overall agonist-antagonist behavior. The FFAR1 system, free fatty acid receptor 1, of which some crystallographic structures of agonists and antagonists are available, will be shown as an example.

L'articolo si pone l'obiettivo di analizzare dal punto di vista storico-linguistico e metrico-stilistico una delle prime traduzioni di Mario Praz dalla lingua inglese e di ricostruire un quadro generale riguardante il suo metodo di traduzione. Si è scelta la traduzione del Corvo di Edgar Allan Poe poiché in essa si vedono in embrione tutti i procedimenti traduttivi che andranno poi a comporre le linee guida che Praz sempre seguirà nelle proprie rese in lingua italiana. Scelte caratterizzate, come risulta da un'analisi dei testi critici nei quali l'autore riflette sulla sua teoria di traduzione, dal continuo tentativo di individuare e rendere nella lingua d'arrivo le dominanti che costituiscono le principali ragioni di composizione e la posizione culturale che il testo da tradurre ricopre nella lingua di partenza. Nel tradurre Il Corvo Praz decide perciò di mantenere quanto più possibile la forma metrica dell'originale, adattandola al sistema versificatorio italiano; inoltre ricalca il complicato schema rimico e le continue tessiture foniche del testo originale mentre dal punto di vista linguistico fa una serie di scelte volte a richiamare il linguaggio arcaizzante di Poe. Esito finale della traduzione è un testo che si avvicina all'atmosfera dell'originale, trasponendone insieme il fascino e alcuni limiti poetici.