Recent developments and applications of the MMPBSA method
The Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) approach has been
widely applied as an efficient and reliable free energy simulation method to model molecular …
widely applied as an efficient and reliable free energy simulation method to model molecular …
Designing a bioadjuvant candidate vaccine targeting infectious bursal disease virus (IBDV) using viral VP2 fusion and chicken IL-2 antigenic epitope: A bioinformatics …
S Soleymani, F Janati-Fard… - Computers in Biology and …, 2023 - Elsevier
Abstract Infectious Bursal Disease (IBD) is a common and contagious viral infection that
significantly affects the poultry industry. This severely suppresses the immune system in …
significantly affects the poultry industry. This severely suppresses the immune system in …
A molecular dynamic study on the ability of phosphorene for designing new sensor for SARS-CoV-2 detection
Due to the dramatic increase in the number of patients with severe acute respiratory
syndrome coronavirus 2 (SARS-CoV-2), designing new selective and sensitive sensors for …
syndrome coronavirus 2 (SARS-CoV-2), designing new selective and sensitive sensors for …
On the Sensitivity and Affinity of Gold, Silver, and Platinum Surfaces against the SARS-CoV-2 Virus: A Comparative Computational Study
M Khavani, A Mehranfar… - Journal of Chemical …, 2023 - ACS Publications
The novel coronavirus disease and its complications have motivated the design of new
sensors with the highest sensitivity, and affinity for the detection of the SARS-CoV-2 virus is …
sensors with the highest sensitivity, and affinity for the detection of the SARS-CoV-2 virus is …
Theoretical design and experimental study of new aptamers with the improved target-affinity: New insights into the Pb2+-specific aptamers as a case study
This study introduces a screening method to design the new aptamers (mutants) with an
improved target specificity by using a joint of theoretical and experimental study. The …
improved target specificity by using a joint of theoretical and experimental study. The …
The investigation of the G-quadruplex aptamer selectivity to Pb2+ ion: a joint molecular dynamics simulation and density functional theory study
The aptamers with the ability to form a G-quadruplex structure can be stable in the presence
of some ions. Hence, study of the interactions between such aptamers and ions can be …
of some ions. Hence, study of the interactions between such aptamers and ions can be …
DFT study on the selective complexation of B12N12 nanocage with alkali metal ions
Density functional theory (DFT) calculations were applied at the M05-2X/6-311++ G (d, p)
level of the theory to investigate the interaction of the B12N12 nanocage (BN) and alkali …
level of the theory to investigate the interaction of the B12N12 nanocage (BN) and alkali …
The effects of amino acid sequence and solvent polarity on the self-assembling of cyclic peptide nanotubes and molecular channel formation inside the lipid bilayer
In this article, the effects of amino acid sequence and solvent polarity on the self-assembling
process of cyclic peptides (CPs) were investigated by employing molecular dynamic (MD) …
process of cyclic peptides (CPs) were investigated by employing molecular dynamic (MD) …
Molecular analyses of the c-terminal craf variants associated with cardiomyopathy reveal their opposing impacts on the active conformation of the kinase domain
S Nakhaei-Rad, F Janatifard, R Dvorsky… - Journal of …, 2023 - Taylor & Francis
The germline mutations in the C-terminus of CRAF kinase, particularly L603, and
S612T/L613V, are associated with congenital heart disorders, for example, dilated …
S612T/L613V, are associated with congenital heart disorders, for example, dilated …
Temperature and molecular crowding effects on the sensitivity of T30695 aptamer toward Pb2+ ion: a joint molecular dynamics simulation and experimental study
The aptamer-target binding affinity can be influenced by some environmental parameters,
eg temperature and molecular crowding agents. Molecular dynamics (MD) simulation is a …
eg temperature and molecular crowding agents. Molecular dynamics (MD) simulation is a …