Functional analysis of the binding model of microbial inulinases using docking and molecular dynamics simulation.

abstract：:Carbon monoxide (CO) and oxygen (O2) catalyzed by small neutral iron oxide clusters (FeO(1-3)) was investigated at the density functional level of theory using the Becke-Perdew-Wang functional (BPW91). Three reaction pathways along with singlet, triplet and quintet states were calculated for ascertaining the presence ...

journal_title：Journal of molecular modeling

authors： Wang HJ,Wang YC

更新日期：2014-06-01 00:00:00

abstract：:Beta-lactamase (ampC) in general causes the onset of antibiotic resistance in pathogenic bacteria against the β-lactam antibiotics. Morganella morganii which belongs to the Proteae tribe of the Enterobacteriaceae family is a Gram-negative bacillus. Gram-negative bacteria are the key problematic agents among the human ...

journal_title：Journal of molecular modeling

authors： Alazmi M

更新日期：2020-07-07 00:00:00

abstract：:The first and second moment operators are used to define the origin invariant shape and size of a molecule or functional group, as well as expressions for the distance between two electrons and the distance between an electron and a nucleus. The measure of molecular size correlates quite well with an existing theoreti...

journal_title：Journal of molecular modeling

authors： Hollett JW,Poirier RA

更新日期：2009-06-01 00:00:00

abstract：:Checkpoint kinase 1 (Chk1), a member of the serine/threonine kinase family, is an attractive therapeutic target for anticancer combination therapy. A structure-based modeling approach complemented with shape components was pursued to develop a reliable pharmacophore model for ATP-competitive Chk1 inhibitors. Common ch...

journal_title：Journal of molecular modeling

authors： Chen XM,Lu T,Lu S,Li HF,Yuan HL,Ran T,Liu HC,Chen YD

更新日期：2010-07-01 00:00:00

abstract：:A density functional theory augmented by the long-range corrected hybrid density functional ωB97XD and 6-31G(d,p) basis set has been applied to generate sandwich structures consist of nanocomposites between graphene oxide and polyvinyl alcohol. We predicted the interaction energies and discuss the contribution of elec...

journal_title：Journal of molecular modeling

authors： Gorb L,Ilchenko M,Leszczynski J

更新日期：2020-06-25 00:00:00

abstract：:The mechanism for the hydroxyl-radical-induced depolymerization of cellulose under alkaline conditions in air was investigated using density functional theory at the B3LYP/6-31+G(d,p) level as well as electron transfer theory. The pathway for the depolymerization of cellulose was obtained theoretically and H abstracti...

journal_title：Journal of molecular modeling

authors： Shao C,Shi K,Hua Q,Zhang L,Dai Y,You W,Liu Y,Li C,Zhang C

更新日期：2018-05-02 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 aquatic leech, Theromyzon tessulatum, secretes a proteinaceous cocoon with extraordinary physical properties (e.g., proteolytic, thermal resiliency). The deduced amino acid sequence of a major protein (Tcp-Theromyzon cocoon protein) from the T. tessulatum cocoon wall has been used to model the endogenous structure...

journal_title：Journal of molecular modeling

authors： Mason TA,McIlroy PJ,Shain DH

更新日期：2006-09-01 00:00:00

abstract：:We tested different approaches to including the effect of binding-site water molecules for ligand-binding affinities within the MM/GBSA approach (molecular mechanics combined with generalised Born and surface-area solvation). As a test case, we studied the binding of nine phenol analogues to ferritin. The effect of wa...

journal_title：Journal of molecular modeling

authors： Mikulskis P,Genheden S,Ryde U

更新日期：2014-06-01 00:00:00

abstract：:Three-dimensional pharmacophore models of human adenosine receptor A(₂A) antagonists were developed based on 23 diverse compounds selected from a large number of A(₂A) antagonists. The best pharmacophore model, Hypo1, contained five features: one hydrogen bond donor , three hydrophobic points and one ring aromatic. It...

journal_title：Journal of molecular modeling

authors： Xu Z,Cheng F,Da C,Liu G,Tang Y

更新日期：2010-12-01 00:00:00

abstract：:The intercalation process and the structure of montmorillonite intercalated with [rhodamine B]+ cations have been investigated using molecular modeling (molecular mechanics and molecular dynamics simulations), X-ray powder diffraction and IR spectroscopy. The structure of the intercalate depends strongly on the concen...

journal_title：Journal of molecular modeling

authors： Pospísil M,Capková P,Weissmannová H,Klika Z,Trchová M,Chmielová M,Weiss Z

更新日期：2003-02-01 00:00:00

abstract：:D222G mutation of the hemagglutinin (HA) is of special interest because of its close association with the enhanced virulence of 2009 pandemic influenza A (H1N1) virus through the increased binding affinity to α2,3-linked sialylated glycan receptors. However, there is still a lack of detailed understanding about the mo...

journal_title：Journal of molecular modeling

authors： Pan D,Xue W,Wang X,Guo J,Liu H,Yao X

更新日期：2012-09-01 00:00:00

abstract：:Quantum chemical calculations using density functional theory BP86/def2-TZVPP and ab initio methods at CCSD(T)/def2-TZVPP have been carried for the telluroketones H2A=Te (A = C, Si, Ge). DFT calculations have also been carried out for the ketones H2C=E (E = O, S, Se, Te) and for the complexes NHC → [H2A=Te] → B(C6F5)3...

journal_title：Journal of molecular modeling

authors： Jaufeerally NB,Ramasami P,Jerabek P,Frenking G

更新日期：2014-10-01 00:00:00

abstract：:Studying the electrochemical characteristics is an important step for determining interactions between molecules and the chemical environment. Moreover, the electrochemical evaluation of dyes is highly needed to establish the behavior of electro-active chemical species inside dye-sensitized solar cells (DSSCs). Four c...

journal_title：Journal of molecular modeling

authors： Ortega E,Bernède JC,Ramírez AMR,Louarn G,Díaz FR,Cattin L,Del Valle MA

更新日期：2019-02-27 00:00:00

abstract：:To improve understanding of the unimolecular decomposition mechanism of 1,2,4-butanetriol trinitrate (BTTN) in the gas phase, density functional theory calculations were performed to determine various decomposition pathways at the B3LYP/6-311G** level. Two main mechanisms for the unimolecular decomposition of BTTN wer...

journal_title：Journal of molecular modeling

authors： Zhu W,Yan Q,Pang A,Chi X,Du X,Xiao H

更新日期：2014-02-01 00:00:00

abstract：:Ethanol and water are the solvents most commonly used to extract flavonoids from propolis. Do hydrogen-bonding interactions exist between flavonoids and ethanol/water? In this work, this question was addressed by using density functional theory (DFT) to provide information on the hydrogen-bonding interactions between ...

journal_title：Journal of molecular modeling

authors： Zheng YZ,Zhou Y,Liang Q,Chen DF,Guo R

更新日期：2016-04-01 00:00:00

abstract：:Molecular simulations were carried out to study the sodium dodecyl sulfate (SDS) surfactant with the interleukin 8 (IL8) protein as a model to investigate the influence of amphiphilic molecules on proteins. Simulations for an SDS micelle with an IL8 protein show that both aggregates, which were initially separated, ev...

journal_title：Journal of molecular modeling

authors： Dominguez H

更新日期：2017-07-01 00:00:00

abstract：:The present study reports the geometry, electronic structure and properties of neutral and anionic transition metal (TM = Ti, Zr and Hf)) doped germanium clusters containing 1 to 20 germanium atoms within the framework of linear combination of atomic orbitals density functional theory under spin polarized generalized ...

journal_title：Journal of molecular modeling

authors： Kumar M,Bhattacharyya N,Bandyopadhyay D

更新日期：2012-01-01 00:00:00

abstract：:Clindamycin, a lincosamide antibiotic, binds to 23S ribosomal RNA and inhibits protein synthesis. The A2058G mutation in 23S RNA results in bacterial resistance to clindamycin. To understand the influence of this mutation on short-range interactions of clindamycin with 23S RNA, we carried out full-atom molecular dynam...

journal_title：Journal of molecular modeling

authors： Kulczycka-Mierzejewska K,Sadlej J,Trylska J

更新日期：2018-07-03 00:00:00

abstract：:Using density functional theory (DFT) and molecular dynamics (MD), we studied the interaction of a titanium atom with a half of a C60 fullerene (i.e., C30), formed from the corannulene structure with a pentagonal base. We considered atmospheric pressure and 300 K. We found that the most stable adsorption of the titani...

journal_title：Journal of molecular modeling

authors： Canales M,Ramírez-de-Arellano JM,Magana LF

更新日期：2016-09-01 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 binding of the reductase inhibitor drug fluvastatin, hydroxy-3-methylglutaryl coenzyme A, with the hydrophilic ι- or λ-carrageenan polymers, serving as potential controllers of the drug's release rate, have been studied at the density functional level of theory with the B3LYP exchange correlation functional. Three...

journal_title：Journal of molecular modeling

authors： Papadopoulos AG,Sigalas MP

更新日期：2011-07-01 00:00:00

abstract：:The nature of non-covalent interactions in self-assembling systems is a topic that has aroused great attention in literature. In this field, the 1,3,5-triazinane-2,4,6-trione or cyanuric acid (CA) is one of the most widely used molecules to formulate self-assembled materials or monolayers. In the present work, a varie...

journal_title：Journal of molecular modeling

authors： Petelski AN,Peruchena NM,Pamies SC,Sosa GL

更新日期：2017-08-14 00:00:00

abstract：:In recent years, several new chelating reagents have been synthesized and tested for their collecting power in sulfide and non-sulfide minerals flotation. Many researchers have indicated that chelating reagents have the advantage of offering better selectivity and specificity as flotation collectors. Therefore, densit...

journal_title：Journal of molecular modeling

authors： Yekeler H,Yekeler M

更新日期：2006-09-01 00:00:00

abstract：:The substituted effect on excited-state intramolecular proton transfer (ESIPT) of o-LHBDI derivatives (4R-o-LHBDI) was investigated by DFT and TD-DFT methods. The structures of 4R-o-LHBDI (R: OH, NH2, CN, NO2, CF3) were fully optimized, and the H-bond distances, bond angles, and infrared spectra of the atoms involved ...

journal_title：Journal of molecular modeling

authors： Ni M,Su S,Fang H

更新日期：2020-04-23 00:00:00

abstract：:The total energies, growth patterns, equilibrium geometries, relative stabilities, hardnesses, intramolecular charge transfer, and magnetic moments of HoSi n (n = 12-20) clusters have been reexamined theoretically using two different density functional schemes in combination with relativistic small-core Stuttgart effe...

journal_title：Journal of molecular modeling

authors： Hou L,Yang J,Liu Y

更新日期：2016-08-01 00:00:00

abstract：:Ab initio (MP2) and DFT (B3LYP) calculations, using the cc-pVTZ and aug-cc-pVTZ basis sets, have been performed to characterize some stationary points on the ground state potential energy surface of the title molecules. Several properties as, for instance, relative energies, the barriers for NO rotation around the NN ...

journal_title：Journal of molecular modeling

authors： do Monte SA,de Andrade RB,Ventura E,de Santana SR

更新日期：2012-01-01 00:00:00

abstract：:Theoretical investigation of Pt(0)-olefin organometallic complexes containing tertiary phosphine ligands was focused on the strength of platinum-olefin electronic interaction. DFT theoretical study of electronic effects in a substantial number of ethylene derivatives was evaluated in terms of the Pt-olefin binding ene...

journal_title：Journal of molecular modeling

authors： Karhánek D,Kacer P,Kuzma M,Splíchalová J,Cervený L

更新日期：2007-09-01 00:00:00

abstract：:Recently, great attention has been focused on using epoxy polymers in different fields such as aerospace, automotive, biotechnology, and electronics, owing to their superior properties. In this study, the classical molecular dynamics (MD) was used to simulate the cross linking of diglycidyl ether of bisphenol-A (DGEBA...

journal_title：Journal of molecular modeling

authors： Shokuhfar A,Arab B

更新日期：2013-09-01 00:00:00

abstract：:B-C binary monolayers and fullerenes (borafullerenes) have received considerable attention in recent years. Inspired by the newly reported B4C3 semiconducting boron carbide monolayer isovalent to graphene (Tian et al., Nanoscale, 2019, 11, 11099), we predict herein at density functional theory level a new class of bor...

journal_title：Journal of molecular modeling

authors： Yan M,Tian XX,Pei L,Ma YY,Zan WY,Mu YW,Li SD

更新日期：2020-07-07 00:00:00