Interaction between shrimp and white spot syndrome virus through PmRab7-VP28 complex: an insight using simulation and docking studies.

abstract：:Vertical ionization energies (VIEs) of medazepam, nordazepam and their molecular subunits have been calculated using the electron propagator method in the P3/CEP-31G* approximation. Vertical electron affinities (VEAs) have been obtained with a ∆SCF procedure at the DFT-B3LYP/6-31+G* level of theory. Excellent correlat...

journal_title：Journal of molecular modeling

authors： Millefiori S,Alparone A

更新日期：2011-02-01 00:00:00

abstract：:4'-substituted neutral/protonated furfurylidenanilines and trans-styrylfurans are able to exist in two different conformations related to the rotation around the furan ring-bridge double bond. In this work, the equilibrium geometry and the corresponding rotational barrier of the benzene ring for each furan derivative ...

journal_title：Journal of molecular modeling

authors： Santos-Carballal D,Suardíaz R,Crespo-Otero R,González L,Pérez CS

更新日期：2013-10-01 00:00:00

abstract：:The heats of formation (HOFs), electronic structure, energetic properties, and thermal stabilities for a series of 1,4-bis(1-azo-2,4-dinitrobenzene)-iminotetrazole derivatives with different substituents and substitution positions and numbers of nitrogen atoms in the nitrobenzene rings were studied using the DFT-B3LYP...

journal_title：Journal of molecular modeling

authors： Wu Q,Pan Y,Zhu W,Xiao H

更新日期：2013-04-01 00:00:00

abstract：:The crystal structure of the human cystatin C (hCC) dimer revealed that a stable twofold-symmetric dimer was formed via 3D domain swapping. Domain swapping with the need for near-complete unfolding has been proposed as a possible route for amyloid fibril initiation. Thus, the interesting interactions that occur betwee...

journal_title：Journal of molecular modeling

authors： He J,Xu L,Zhang S,Guan J,Shen M,Li H,Song Y

更新日期：2013-02-01 00:00:00

abstract：:The density functional theory method using the B3LYP/6-31G(d,p) level of theory was used to perform isoenergetic maps in order to determine the lower energy conformers of four disaccharides constituting alginic acids, which are based on β-D-mannuronic (M) and α-L-guluronic acid (G), called MM, GG, MG, and GM. The pref...

journal_title：Journal of molecular modeling

authors： Bekri L,Zouaoui-Rabah M,Springborg M,Rahal MS

更新日期：2018-10-10 00:00:00

abstract：:The mechanism of the cycloaddition reaction CH3M≡MCH3 (M=C, Si, Ge) with C2H4 has been studied at the CCSD(T)/6-311++G(d,p)//MP2/6-311++G(d,p) level. Vibrational analysis and intrinsic reaction coordinate (IRC), calculated at the same level, have been applied to validate the connection of the stationary points. The br...

journal_title：Journal of molecular modeling

authors： Huo S,Li X,Zeng Y,Zheng S,Meng L

更新日期：2013-09-01 00:00:00

abstract：:We present an ab initio based molecular mechanics model for prominent additives used in lubricants to moderate oil-steel interfaces. The force field is created for zinc dialkyldithiophosphate and calcium sulfonate charge neutral ligand-ion-ligand complexes and benchmarked to the widely spread generalized amber force f...

journal_title：Journal of molecular modeling

authors： Ectors P,Zahn D

更新日期：2019-03-25 00:00:00

abstract：:The Fbw7-Skp1 complex is an essential component in the formation and development of the mammalian cardiovascular system; the complex interaction is mediated through binding of Skp1 C-terminal peptide (qGlu-peptide) to the F-box domain of Fbw7. By visually examining the crystal structure, we identified a typical cation...

journal_title：Journal of molecular modeling

authors： Zhou J,Wang YS

更新日期：2017-09-26 00:00:00

abstract：:A quantum mechanical density functional theory (DFT) was successfully developed for the estimation of pKa values of chlorinated phenols in aqueous solution with a precision of 0.9 pKa units. The MP2/6-311++G(d,p)//B3LYP/6-31+G(d) level of theory was used for the gas phase calculation. For computation in the solution p...

journal_title：Journal of molecular modeling

authors： Kheirjou S,Imanzadeh G,Rezaei H,Safari N

更新日期：2019-06-26 00:00:00

abstract：:Eleven 1,4-naphthoquinone analogues with different amino substitutions at position 3 of the quinone ring earlier reported for macrofilaricidal activity were selected and screened against purified cytosolic GST isolated from the bovine filarial worm Setaria digitata and IC(50) values were determined. Of the 11 compound...

journal_title：Journal of molecular modeling

authors： Mathew N,Srinivasan L,Karunan T,Ayyanar E,Muthuswamy K

更新日期：2011-10-01 00:00:00

abstract：:The theoretical three-dimensional structure of a novel δ-endotoxin Cry1Id (81 kDa) belonging to Cry1I class, toxic to many of the lepidopteran pests has been investigated through comparative modeling. Molecular dynamics (MD) simulations was carried out to characterize its structural and dynamical features at 10 ns in ...

journal_title：Journal of molecular modeling

authors： Dehury B,Sahu M,Sahu J,Sarma K,Sen P,Modi MK,Barooah M,Choudhury MD

更新日期：2013-12-01 00:00:00

abstract：:CD44 is a cell-surface glycoprotein and receptor for hyaluronan, one of the major components of the tumor extracellular matrix. There is evidence that the interaction between CD44 and hyaluronan promotes breast cancer metastasis. Recently, the molecule F-19848A was shown to inhibit hyaluronan binding to receptor CD44 ...

journal_title：Journal of molecular modeling

authors： Nguyen TT,Tran DP,Pham Dinh Quoc Huy,Hoang Z,Carloni P,Van Pham P,Nguyen C,Li MS

更新日期：2016-07-01 00:00:00

abstract：:Multilayer-shaped compression and slide models were employed to investigate the complex sensitive mechanisms of cocrystal explosives in response to external mechanical stimuli. Here, density functional theory (DFT) calculations implementing the generalized gradient approximation (GGA) of Perdew-Burke-Ernzerhof (PBE) w...

journal_title：Journal of molecular modeling

authors： Gao HF,Zhang SH,Ren FD,Gou RJ,Han G,Wu JB,Ding X,Zhao WH

更新日期：2016-05-01 00:00:00

abstract：:Monoamine oxidase (MAO) is an enzyme of major importance in neurochemistry, because it catalyzes the inactivation pathway for the catecholamine neurotransmitters, noradrenaline, adrenaline and dopamine. In the last decade it was demonstrated that imidazoline derivatives were able to inhibit MAO activity. Furthermore, ...

journal_title：Journal of molecular modeling

authors： Moraes FP,de Azevedo WF Jr

更新日期：2012-08-01 00:00:00

abstract：:Understanding how temperature affects the electronic transitions of BFO is important for design of BiFeO3 (BFO)-based temperature-sensitive device. Hitherto, however, there have been only very limited reports of the quantitative simulation. Here, we used density functional theory (DFT) and two-dimensional correlation ...

journal_title：Journal of molecular modeling

authors： Bian L,Xu JB,Song MX,Dong FQ,Dong HL,Shi FN,Zhang XY,Duan T

更新日期：2015-04-01 00:00:00

abstract：:Acene-thiophenes compounds have been used successfully as active materials in thin-film transistors and photodetectors. This work aims at obtaining an adequate theoretical framework to accurately characterize the optical and electronic properties of two such compounds: NaT2 and NaT3. This is done by comparing the resu...

journal_title：Journal of molecular modeling

authors： de Sousa LE,Mamiya AA,Kjelstrup-Hansen J,da Silva Filho DA

更新日期：2017-02-01 00:00:00

abstract：:Several cellular disorders have been related to the overexpression of the cysteine protease cathepsin B (CatB), such as rheumatic arthritis, muscular dystrophy, osteoporosis, Alzheimer's disease, and tumor metastasis. Therefore, inhibiting CatB may be a way to control unregulated cellular functions and prevent tissue ...

journal_title：Journal of molecular modeling

authors： Vega-Teijido MA,El Chamy Maluf S,Bonturi CR,Sambrano JR,Ventura ON

更新日期：2014-06-01 00:00:00

abstract：:The UV absorption spectra of ten N,N'-bisarylmalonamides have been recorded in the range 200-400 nm in a set of selected solvents. The solute-solvent interactions have been analyzed on the basis of the linear solvation energy relationship (LSER) concept proposed by Kamlet and Taft. The effects of substituents on the a...

journal_title：Journal of molecular modeling

authors： Arsovski VM,Božić BĐ,Mirković JM,Vitnik VD,Vitnik ZJ,Fabian WM,Petrović SD,Mijin DZ

更新日期：2014-08-01 00:00:00

abstract：:The original version of this article unfortunately contained a mistake. Schemes I and II were missing. These important components are given below. ...

journal_title：Journal of molecular modeling

authors： Roy RS,Mondal A,Nandi PK

更新日期：2017-11-01 00:00:00

abstract：:The burial of hydrophobic amino acids in the protein core is a driving force in protein folding. The extent to which an amino acid interacts with the solvent and the protein core is naturally proportional to the surface area exposed to these environments. However, an accurate calculation of the solvent-accessible surf...

journal_title：Journal of molecular modeling

authors： Durham E,Dorr B,Woetzel N,Staritzbichler R,Meiler J

更新日期：2009-09-01 00:00:00

abstract：:The aim of the present work entitled electronic structure of PVA-PEG-Y2O3 (54 atom) is to present a theoretical study based on the hybrid function of three parameters Lee-Yang-Parr B3LYP of the density functional theory "DFT" quantum mechanical approach together with LanL2DZ basis sets for optoelectronics applications...

journal_title：Journal of molecular modeling

authors： Ahmed H,Hashim A

更新日期：2020-07-20 00:00:00

abstract：:The mechanism of the copper(I)-catalyzed cyclopropanation reaction for methyl diazoacetate with both (Z)- and (E)-but-2-ene stereoisomers has been studied using the 6-311++G(d,p) basis set by means of M06-2X and O3LYP functionals. According to both methods, the rate-limiting step is the formation of a copper-carbene i...

journal_title：Journal of molecular modeling

authors： Angulo B,Herrerías CI,Hormigón Z,Mayoral JA,Salvatella L

更新日期：2018-07-05 00:00:00

abstract：:Trinitromethyl-substituted aminotetrazoles with -NH₂, -NO₂, -N₃, and -NHC(NO₂)₃ groups were investigated at the B3LYP/6-31G(d) level of density functional theory. Their sublimation enthalpies, thermodynamic properties, and heats of formation were calculated. The thermodynamic properties of these compounds increase wit...

journal_title：Journal of molecular modeling

authors： Lin H,Chen PY,Zhu SG,Zhang L,Peng XH,Li K,Li HZ

更新日期：2013-06-01 00:00:00

abstract：:In this work we report the atomic partial charges evaluated on dodecyltrimethylammonium ion. The values obtained from 17 quantum methods [CHELP, CHELPG, MK, NPA at (HF, LDA, PBE, B3LYP)//6-31G++(d,p) level and APT at B3LYP//6-31G++(d,p)] on the molecule optimised at B3LYP/6-31G++(d,p) level were compared to two semiem...

journal_title：Journal of molecular modeling

authors： Minisini B,Chavand S,Barthelery R,Tsobnang F

更新日期：2010-06-01 00:00:00

abstract：:The chain tacticity of a polymer is a key influence on its structure and dynamics, which ultimately determine its properties. While they have great potential to elucidate the influence of chain tacticity, all-atom molecular simulations are often restricted to short chains and small systems. In this work, two typical s...

journal_title：Journal of molecular modeling

authors： Wu C

更新日期：2014-08-01 00:00:00

abstract：:Knowledge-based models for protein folding assume that the early-stage structural form of a polypeptide is determined by the backbone conformation, followed by hydrophobic collapse. Side chain-side chain interactions, mostly of hydrophobic character, lead to the formation of the hydrophobic core, which seems to stabil...

journal_title：Journal of molecular modeling

authors： Brylinski M,Kochanczyk M,Broniatowska E,Roterman I

更新日期：2007-07-01 00:00:00

abstract：:The adsorption behavior of sulfur-based toxic gases (H2S and SO2) on armchair silicene nanoribbons (ASiNRs) was investigated using first-principles density functional theory (DFT). Being a zero band gap material, application of bulk silicene is limited in nanoelectronics, despite its high carrier mobility. By restrict...

journal_title：Journal of molecular modeling

authors： Walia GK,Randhawa DKK

更新日期：2018-03-16 00:00:00

abstract：:The conformational analysis of polynorbornene (PNB) chains was investigated with the AM1, MM2, AMBER and OPLS methods taking into consideration the possibility of binding of norbornene monomers to each other at various positions, i.e. exo-exo, exo-endo, endo-endo. The chain that is formed by connecting exo-endo positi...

journal_title：Journal of molecular modeling

authors： Yilmaz SS,Abbasoğlu R,Hazer B

更新日期：2003-08-01 00:00:00

abstract：:The virtual combinatorial chemistry approach as a methodology for generating chemical libraries of structurally-similar analogs in a virtual environment was employed for building a general mixed virtual combinatorial library with a total of 53.871 6-FQ structural analogs, introducing the real synthetic pathways of thr...

journal_title：Journal of molecular modeling

authors： Minovski N,Perdih A,Solmajer T

更新日期：2012-05-01 00:00:00

abstract：:The ability to accurately predict the oxidation and reduction potentials of molecules is very useful in various fields and applications. Quantum mechanical calculations can be used to access this information, yet sometimes the usefulness of these calculations can be limited because of the computational requirements fo...

journal_title：Journal of molecular modeling

authors： Méndez-Hernández DD,Tarakeshwar P,Gust D,Moore TA,Moore AL,Mujica V

更新日期：2013-07-01 00:00:00