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Structure and functional dynamics characterization of the ion channel of the human respiratory syncytial virus (hRSV) small hydrophobic protein (SH) transmembrane domain by combining molecular dynamics with excited normal modes
(Springer, 2016-12-01)
The human respiratory syncytial virus (hRSV) is the major cause of lower respiratory tract infection in children and elderly people worldwide. Its genome encodes 11 proteins including SH protein, whose functions are not ...
Lessons learned about steered molecular dynamics simulations and free energy calculations
(Wiley Blackwell Publishing, Inc, 2019-01)
The calculation of free energy profiles is central in understanding differential enzymatic activity, for instance, involving chemical reactions that require QM-MM tools, ligand migration, and conformational rearrangements ...
The shoving model for the glass-former LiCl center dot 6H(2)O: A molecular dynamics simulation study
(ELSEVIER SCIENCE BV, 2009)
Molecular dynamics (MD) simulations of LiCl center dot 6H(2)O Showed that the diffusion coefficient D, and also I lie structural relaxation time <tau >, follow a power law at high temperatures, D(-1) proportional to (T - ...
Effect of pH on Eosin Y/PAMAM interactions studied from absorption spectroscopy and molecular dynamics simulations
(Elsevier Science, 2018-07)
Absorption spectroscopy experiments were carried out to examine the 1:1 supramolecular interaction between Eosin Y (EOS) and low generation G0-G3 poly(amido amine) (PAMAM) dendrimers at neutral and basic media, aimed at ...
RIP-MD: a tool to study residue interaction networks in protein molecular dynamics
(PEERJ INC, 2018)
Protein structure is not static; residues undergo conformational rearrangements and, in doing so, create, stabilize or break non-covalent interactions. Molecular dynamics (MD) is a technique used to simulate these movements ...
The redundancy of NMR restraints can be used to accelerate the unfolding behavior of an SH3 domain during molecular dynamics simulations
(BioMed CentralLondon, 2011-11)
Background:
The simulation of protein unfolding usually requires recording long molecular dynamics trajectories. The present work aims to figure out whether NMR restraints data can be used to probe protein conformations ...
Structural characterization of the saxitoxin-targeting APTSTX1 aptamer using optical tweezers and molecular dynamics simulations.
Optical tweezers have enabled the exploration of picoNewton forces and dynamics in single–molecule systems such as DNA and molecular motors. In this work, we used optical tweezers to study the folding/unfolding dynamics ...
Computer simulations of the solvation dynamics of Coumarin 153 in dimethylsulfoxide
(Elsevier Science BvAmsterdamHolanda, 2003)
Intermediate structures for higher level arrangements: catching disk-like micelles in decane phosphonic acid aqueous solutions
(American Chemical Society, 2013-04)
It has been proposed that disk-like micelles may be precursors to the formation of lamellar liquid crystals. The possibility of obtaining n-decane phosphonic acid (DPA) disklike micelles in aqueous solution without the ...
Applying Computer Simulations in Battling with COVID-19, using pre-analyzed molecular and chemical data to face the pandemic
Coronavirus disease 2019 (COVID-19) has made many concerns for healthcare services especially, in finding useful therapeutic(s). Despite the scientists’ struggle to find and/or creating possible drugs, so far there is no ...