Evaluation of Sox2 binding affinities for distinct DNA patterns using steered molecular dynamics simulation
Sign Up to like & getrecommendations! Published in 2017 at "FEBS Open Bio"
DOI: 10.1002/2211-5463.12316
Abstract: Transcription factors (TFs) are gene expression regulators that bind to DNA in a sequence‐specific manner and determine the functional characteristics of the gene. It is worthwhile to study the unique characteristics of such specific TF‐binding… read more here.
Keywords: dna; molecular dynamics; distinct dna; steered molecular ... See more keywords
Steered molecular dynamics simulation of the binding of the bovine auxilin J domain to the Hsc70 nucleotide-binding domain
Sign Up to like & getrecommendations! Published in 2017 at "Journal of Molecular Modeling"
DOI: 10.1007/s00894-017-3453-2
Abstract: The Hsp70 and Hsp40 chaperone machine plays critical roles in protein folding, membrane translocation, and protein degradation by binding and releasing protein substrates in a process that utilizes ATP. The activities of the Hsp70 family… read more here.
Keywords: auxilin domain; molecular dynamics; auxilin; steered molecular ... See more keywords
The effects of mutation on the drug binding affinity of Neuraminidase: case study of Capsaicin using steered molecular dynamics simulation
Sign Up to like & getrecommendations! Published in 2022 at "Journal of Molecular Modeling"
DOI: 10.1007/s00894-021-05005-7
Abstract: The influenza virus is an important respiratory pathogen that causes many incidences of diseases and even death each year. One of the primary factors of this virus is the Neuraminidase surface protein, which causes the… read more here.
Keywords: steered molecular; using steered; affinity; drug ... See more keywords
Implementation of Telescoping Boxes in Adaptive Steered Molecular Dynamics.
Sign Up to like & getrecommendations! Published in 2022 at "Journal of chemical theory and computation"
DOI: 10.1021/acs.jctc.2c00498
Abstract: Long-time dynamical processes, such as those involving protein unfolding and ligand interactions, can be accelerated and realized through steered molecular dynamics (SMD). The challenge has been the extraction of information from such simulations that generalize… read more here.
Keywords: implementation telescoping; telescoping boxes; adaptive steered; boxes adaptive ... See more keywords
Accelerated Construction of Kinetic Network Model of Biomolecules Using Steered Molecular Dynamics.
Sign Up to like & getrecommendations! Published in 2018 at "Journal of chemical theory and computation"
DOI: 10.1021/acs.jctc.8b00398
Abstract: A new class of rare event acceleration techniques based on steered molecular dynamics (SMD) simulations is introduced. A stretching force applied on a biomolecule causes it to access large end-to-end distances. Under these conditions the… read more here.
Keywords: force conditions; molecular dynamics; master msm; model ... See more keywords
Massively Parallel Implementation of Steered Molecular Dynamics in Tinker-HP: Comparisons of Polarizable and Non-Polarizable Simulations of Realistic Systems.
Sign Up to like & getrecommendations! Published in 2019 at "Journal of chemical theory and computation"
DOI: 10.1021/acs.jctc.9b00199
Abstract: Steered molecular dynamic (SMD) is a powerful technique able to accelerate rare event sampling in Molecular Dynamics (MD) simulations by applying an external force to a set of chosen atoms. Despite generating nonequilibrium simulations, SMD… read more here.
Keywords: molecular dynamics; force; tinker; steered molecular ... See more keywords
Random acceleration and steered molecular dynamics simulations reveal the (un)binding tunnels in adenosine deaminase and critical residues in tunnels
Sign Up to like & getrecommendations! Published in 2020 at "RSC Advances"
DOI: 10.1039/d0ra07796h
Abstract: Adenosine deaminase (ADA) is an important enzyme related to purine nucleoside metabolism in human serum and various tissues. Abnormal ADA levels are related to a wide variety of diseases such as rheumatoid arthritis, AIDS, anemia,… read more here.
Keywords: molecular dynamics; ada; steered molecular; adenosine deaminase ... See more keywords
Nanomechanical properties of MscL α helices: A steered molecular dynamics study
Sign Up to like & getrecommendations! Published in 2017 at "Channels"
DOI: 10.1080/19336950.2016.1249077
Abstract: ABSTRACT Gating of mechanosensitive (MS) channels is driven by a hierarchical cascade of movements and deformations of transmembrane helices in response to bilayer tension. Determining the intrinsic mechanical properties of the individual transmembrane helices is… read more here.
Keywords: properties mscl; molecular dynamics; mscl helices; steered molecular ... See more keywords
Computational Study for the Unbinding Routes of β-N-Acetyl-d-Hexosaminidase Inhibitor: Insight from Steered Molecular Dynamics Simulations
Sign Up to like & getrecommendations! Published in 2019 at "International Journal of Molecular Sciences"
DOI: 10.3390/ijms20061516
Abstract: β-N-Acetyl-d-hexosaminidase from Ostrinia furnacalis (OfHex1) is a new target for the design of insecticides. Although some of its inhibitors have been found, there is still no commercial drug available at present. The residence time of… read more here.
Keywords: molecular dynamics; acetyl hexosaminidase; steered molecular; unbinding routes ... See more keywords
Steered Molecular Dynamics Simulations Study on FABP4 Inhibitors
Sign Up to like & getrecommendations! Published in 2023 at "Molecules"
DOI: 10.3390/molecules28062731
Abstract: Ordinary small molecule de novo drug design is time-consuming and expensive. Recently, computational tools were employed and proved their efficacy in accelerating the overall drug design process. Molecular dynamics (MD) simulations and a derivative of… read more here.
Keywords: dynamics simulations; steered molecular; simulations study; molecular dynamics ... See more keywords