Published in Journal of Cheminformatics
In this study we compare the three algorithms for the generation of conformer ensembles Biovia BEST, Schrödinger Prime macrocycle sampling (PMM) and Conformator (CONF) form the University of Hamburg, with ensembles derived for exhaustive molecular dynamics simulations applied to a dataset of 7 small macrocycles in two charge states and three solven...
Published in In Silico Pharmacology
This study is an attempt to find a suitable therapy using antimicrobial peptides (AMPs) by identifying peptide-protein interaction of AMPs and nucleocapsid protein of SARS and SARS-CoV- 2. The AMPs were shortlisted from the APD3 database (Antimicrobial peptide database) based on various physicochemical parameters. The binding efficacy of AMPs was m...
Neste artigo, os comportamentos estrutural e mecânico da liga equiatômica de alta entropia Hf-Nb-Ta-Zr foram estudados mediante simulações computacionais de dinâmica molecular. As simulações foram realizadas no código livre LAMMPS, em um sistema composto de 154.000 átomos que interagiram sob o potencial Embedded Atom Method (EAM). O estudo focou na...
Published in Nanoscale Research Letters
During the nano-cutting process, monocrystalline gallium arsenide is faced with various surface/subsurface deformations and damages that significantly influence the product’s performance. In this paper, molecular dynamics simulations of nano-cutting on gallium arsenide are conducted to investigate the surface and subsurface deformation mechanism. D...
Graphynes are a family of porous carbon allotropes that are viewed as ideal 2D nanofilters. In this present work, the authors have modified the Improved Lennard-Jones (ILJ) semi-empirical potential used in the previous works by adding the induction term (iind) to define the full interaction. The evaluation of the computational cost was done compari...
Published in In Silico Pharmacology
Covid-19 caused by novel coronavirus, 2019-nCoV or SARS-CoV-2 has become most severe pandemic of this century. No specific therapies are available to treat Covid-19 so far. Recently, main protease (Mpro), a potential drug target from SARS-CoV-2 has been successfully crystallised. The present study is aimed at assessment of bioactive antiviral phyto...
Published in Theoretical Chemistry Accounts
Molecular dynamics (MD) simulations are widely used to predict the behavior of molecular systems over time. However, one of the significant challenges of MD simulations is how to treat the thousands of configurations obtained from calculations, since the number of the quantum calculations (QM) required for evaluating electronic parameters is too hi...
Published in Microgravity Science and Technology
In this paper, a collision friction model for a double-layer MoS2 film is proposed considering the microgravity induced collision in space environment. A modified REBO (Reactive Empirical Bond Order) potential is used to describe interactions among the atoms in the MoS2 film. The collision friction process of the MoS2 film is simulated by vibration...
Published in Nature Communications
Determining the structure of amorphous solids is important for optimization of pharmaceutical formulations, but direct relation of molecular dynamics (MD) simulations and NMR to achieve this is challenging. Here, the authors use a machine learning model of chemical shifts to solve the atomic-level structure of the hydrated amorphous drug AZD5718 by...
Published in Journal of biomolecular structure & dynamics
Crystallographic data comes from a space-time average over all the unit cells within the crystal, so dynamic phenomena do not contribute significantly to the diffraction data. Many efforts have been made to reconstitute the movement of the macromolecules and explore the microstates that the confined proteins can adopt in the crystalline network. We...
