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13
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79
Citations
Introduction
Additional affiliations
July 2015 - March 2016
Education
November 2012 - November 2018
Publications
Publications (13)
Significance
Structures of G protein-coupled receptors (GPCRs) in complex with ligands mainly provide frozen pictures with little information about the actual molecular mechanism of action of the ligand in the normally highly dynamic receptor. Through computer-based molecular dynamics simulations of a receptor for long-chain fatty acids, free fatty...
US28 is a broad-spectrum constitutively active G protein-coupled receptor encoded by the human cytomegalovirus (HCMV). It binds and scavenges multiple CC-chemokines as well as CX3CL1 (fractalkine) by constitutive receptor endocytosis to escape immune surveillance. We herein report the design and characterization of a novel library of US28-acting co...
Dopamine as a neurotransmitter plays a critical role in the functioning of the central nervous system. The structure of D3 receptor as a member of class A G-protein coupled receptors (GPCRs) has been reported. We used MD simulation to investigate the effect of an oscillating electric field, with frequencies in the range 0.6–800 GHz applied along th...
Some parameters of dopamine-D3R complex in different directions of oscillating electric field.
(a) Energy of ionic lock, (b) Arg-Glu distance, (c) Energy of D3R, (d) Number of internal hydrogen bond of D3R, (e) Binding free energy of dopamine by applying an external oscillating electric field in different directions ((Z): Electric field along the z...
P-Values of radius of gyration and total dipole of protein in different frequencies.
P-Value<0.05 means that this frequency has a significant effect on radius of gyration or total dipole of protein (Null hypothesis is rejected).
(PDF)
P-Values of different quantities of dopamine-D3R complex in different direction of external oscillating electric field.
P-Value<0.05 means that applying oscillation field in that direction has a significant effect on that quantity (Null hypothesis is rejected).
(PDF)
P-Values of Glu-Arg distance and Broken salt bridge Arg-Glu percentage in different frequencies.
P-Value<0.05 means that this frequency has a significant effect on Glu-Arg distance or Broken salt bridge Arg-Glu percentage (Null hypothesis is rejected).
(PDF)
Different quantities by applying high amplitude of oscillating electric field.
(PDF)
CoZn nanowire were fabricated using alternative-pulse elecrodeposition technique. The effect of various concentrations of Zn ions in electrolyte on composition and magnetic properties of CoZn nanowires was studied. It was found that Co content in CoZn nanowires decreases by increasing Zn concentration in electrolyte. Nanowires with various composit...
CoNi nanowires were deposited by pulsed electrodeposition technique into porous alumina templates. The effect of off time between pulses (t off) and reductive/oxidative time (t reduc/oxid) on the microstructure and magnetic properties of the CoNi nanowires were investigated. Maximum coercivity and squareness were obtained for samples fabricated at...
Questions
Questions (6)
Hello,
I have a script changing the distances of two bonded atoms and I calculated the total energy (or potenial energy, kinetic energy is zero) with energy minimisation tool of lammps (ReaxFF forcfield) but I get the same energy value on step zero of all structures, can anyone help me how we could plot bond dissociation energy using ReaxFF by lammps?
Cheers,
I used gromacs5.0.5 and 5.1 before and now I am using gromacs 5.1.2, but in pullf.xvg, forces were written every time step which was 2 fs but now the forces written every 50 steps, it is while I did not change any thing related to saving steps in mdp file. Now I cannot use both pullf.xvg (I have to use both together), because they do not have the same number of information for gmx wham. Can anyone help me with this?
Hello, I want to apply restrain on ligand in GROMACS5, so I build it with genres and include in topology and define in mdp. But I think it did not work., because ligand move a lot, even with 100000 restrain. I am not sure that the ligand have restrain, how can I be sure? Is applying restrain same in version 5 of GROMACS?
Hi, how can we put restrain/constrain without using freezing for the distance between 2 atoms in ligand and protein with GROMACS5, which these 2 atoms are in different molecules ?
I have a box of one ligand and water in GROMACS,I would like to fix the motion of ligand just in z direction (center of mass of ligand not all its atoms),as I know freezgrps freeze atoms in x,y or z direction,how can we use for center of mass of molecule?
