RPA-1 from Leishmania sp.: Recombinant Protein Expression and Purification, Molecular Modeling, and Molecular Dynamics Simulations Protocols.
Sign Up to like & getrecommendations! Published in 2021 at "Methods in molecular biology"
DOI: 10.1007/978-1-0716-1290-3_10
Abstract: RPA is a conserved heterotrimeric complex and the major single-stranded DNA (ssDNA)-binding protein heterotrimeric complex, which in eukaryotes is formed by the RPA-1, RPA-2, and RPA-3 subunits. The main structural feature of RPA is the… read more here.
Keywords: molecular modeling; rpa leishmania; molecular dynamics; modeling molecular ... See more keywords
Modeling molecular mechanisms in the axon
Sign Up to like & getrecommendations! Published in 2017 at "Computational Mechanics"
DOI: 10.1007/s00466-016-1359-y
Abstract: Axons are living systems that display highly dynamic changes in stiffness, viscosity, and internal stress. However, the mechanistic origin of these phenomenological properties remains elusive. Here we establish a computational mechanics model that interprets cellular-level… read more here.
Keywords: mechanisms axon; level; modeling molecular; molecular mechanisms ... See more keywords
Modeling molecular boiling points using computed interaction energies
Sign Up to like & getrecommendations! Published in 2017 at "Journal of Molecular Modeling"
DOI: 10.1007/s00894-017-3552-0
Abstract: The noncovalent van der Waals interactions between molecules in liquids are typically described in textbooks as occurring between the total molecular dipoles (permanent, induced, or transient) of the molecules. This notion was tested by examining… read more here.
Keywords: boiling points; molecular boiling; modeling molecular; hydrogen bonding ... See more keywords
3D-QSAR modeling and molecular docking studies on a series of 2,5 disubstituted 1,3,4-oxadiazoles
Sign Up to like & getrecommendations! Published in 2017 at "Journal of Molecular Structure"
DOI: 10.1016/j.molstruc.2017.05.065
Abstract: Abstract 3D-QSAR (comparative molecular field analysis (CoMFA)) and comparative molecular similarity indices analysis (CoMSIA) were performed on novel 2,5 disubstituted 1,3,4-oxadiazoles analogues as anti-fungal agents. The CoMFA and CoMSIA models using 13 compounds in the… read more here.
Keywords: docking studies; qsar modeling; modeling molecular; studies series ... See more keywords
Modeling of molecular interaction between catechol and tyrosinase by DFT
Sign Up to like & getrecommendations! Published in 2020 at "Journal of Molecular Structure"
DOI: 10.1016/j.molstruc.2019.127192
Abstract: Abstract In this study, the synthetic active site model of tyrosinase enzyme’s “(His3)Cu..OH..Cu(His3) arrangement” is constituted by applying the density functional theory (DFT) to reveal the enzymatic conversion of catechol in molecular basis. This is… read more here.
Keywords: dft; molecular interaction; modeling molecular; tyrosinase ... See more keywords
Identification of potential human COX-2 inhibitors using computational modeling and molecular dynamics simulations
Sign Up to like & getrecommendations! Published in 2020 at "Journal of Molecular Structure"
DOI: 10.1016/j.molstruc.2020.128271
Abstract: Abstract To explore the structure-property relationship in a set of molecules against Cyclooxygenase-2 (COX-2), pharmacophore modeling, molecular docking and 3D-QSAR studies were performed. A set of 66 reported molecules with different scaffolds having pIC50 values… read more here.
Keywords: molecular dynamics; computational modeling; modeling molecular; cox ... See more keywords
AMOEBA+ Classical Potential for Modeling Molecular Interactions.
Sign Up to like & getrecommendations! Published in 2019 at "Journal of chemical theory and computation"
DOI: 10.1021/acs.jctc.9b00261
Abstract: Classical potentials based on isotropic and additive atomic charges have been widely used to model molecules in computers for the past few decades. The crude approximations in the underlying physics are hindering both their accuracy… read more here.
Keywords: amoeba classical; molecular interactions; potential modeling; modeling molecular ... See more keywords
Modeling Molecular Communications in Tubes With Poiseuille Flow and Robin Boundary Condition
Sign Up to like & getrecommendations! Published in 2019 at "IEEE Communications Letters"
DOI: 10.1109/lcomm.2019.2920830
Abstract: Accurately modeling the molecular channel is crucial for the design and analysis of molecular communications. In this letter, we propose a Markovian-based channel model for molecular communications in tubes with Poiseuille flow and the Robin… read more here.
Keywords: communications tubes; modeling molecular; tubes poiseuille; flow robin ... See more keywords
Modeling the molecular fingerprint of protein-lipid interactions of MLKL on complex bilayers
Sign Up to like & getrecommendations! Published in 2023 at "Frontiers in Chemistry"
DOI: 10.3389/fchem.2022.1088058
Abstract: Lipids, the structural part of membranes, play important roles in biological functions. However, our understanding of their implication in key cellular processes such as cell division and protein-lipid interaction is just emerging. This is the… read more here.
Keywords: lipid interactions; protein lipid; molecular fingerprint; modeling molecular ... See more keywords