Insight into natural inhibitors and bridging docking to dynamic simulation against sugar Isomerase (SIS) domain protein.

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：:A first-principles calculation was carried out to investigate the stability and electronic properties of ultra-thin Cx(BN)y heteronanotubes which were composed by joining pure CNT and BNNT segments with different composition and configurations. We found that the stability of Cx(BN)y heteronanotubes is increased with t...

journal_title：Journal of molecular modeling

authors： Wang Y,Huang G,Zhang J,Shao Q

更新日期：2014-08-01 00:00:00

abstract：:1,3-Dimethylimidazolium dimethylphosphate ([C1mim][DMP]) was observed experimentally to be able to eliminate the atmospheric azeotropic point of acetone and methanol, which is an important azeotrope generally encountered in furfural production and the Fischer-Tropsch process. Here, we employed ab initio calculation to...

journal_title：Journal of molecular modeling

authors： Yu G,Liu X,Zhang X,Chen X,Liu Z,Abdeltawab AA

更新日期：2017-03-01 00:00:00

abstract：:Fruit softening is associated to cell wall modifications produced by a set of hydrolytic enzymes and proteins. Expansins are proteins with no catalytic activity, which have been associated with several processes during plant growth and development. A role for expansins has been proposed during softening of fruits, and...

journal_title：Journal of molecular modeling

authors： Gaete-Eastman C,Morales-Quintana L,Herrera R,Moya-León MA

更新日期：2015-05-01 00:00:00

abstract：:Here, we report a structure-based virtual screening of the ZINC database (containing about five million compounds) by computational docking and the analysis of docking energy calculations followed by in vitro screening against H. pylori urease enzyme. One of the compounds selected showed urease inhibition in the low m...

journal_title：Journal of molecular modeling

authors： Azizian H,Nabati F,Sharifi A,Siavoshi F,Mahdavi M,Amanlou M

更新日期：2012-07-01 00:00:00

abstract：:The ONIOM2 (B3LYP/6-31G (d, p): PM3) and B3LYP/6-31G (d, p) methods were applied to investigate the interaction between STI-571 and abelson tyrosine kinase binding site. The complex of N-[4-methyl-3-(4-pyridin-3-yl-pyrimidin-2-ylamino)- phenyl]-benzamide (part of STI-571) and related 16 amino acid residues were found ...

journal_title：Journal of molecular modeling

authors： Xiong YZ,Chen PY

更新日期：2008-11-01 00:00:00

abstract：:Cyclic nucleotide binding domain (CNBD) is a ubiquitous domain of effector proteins involved in signalling cascades of prokaryota and eukaryota. CNBD activation by cyclic nucleotide monophosphate (cNMP) is studied well in the case of several proteins. However, this knowledge is hardly applicable to cNMP-modulated cati...

journal_title：Journal of molecular modeling

authors： Gushchin IY,Gordeliy VI,Grudinin S

更新日期：2012-09-01 00:00:00

abstract：:PB1-F2 is a recently described influenza A viral protein that induces apoptosis by binding with two mitochondrial membrane proteins, i.e. VDAC1 (outer membrane) and ANT3 (inner membrane). Knowledge of this binding mechanism could provide insights that would aid in the design of novel inhibitors against this protein. T...

journal_title：Journal of molecular modeling

authors： Danishuddin M,Khan SN,Khan AU

更新日期：2010-03-01 00:00:00

abstract：:Since the three-dimensional structure of the NMDA receptor has not been determined experimentally, indirect computer-assisted molecular modeling techniques appear to be of great usefulness in the characterization of the common pharmacophore of all NMDA receptor noncompetitive antagonists, despite their structural diff...

journal_title：Journal of molecular modeling

authors： Elhallaoui M,Laguerre M,Carpy A,Ouazzani FC

更新日期：2002-02-01 00:00:00

abstract：:Hyaluronan lyase from Streptococcus pneumoniae can degrade hyaluronic acid, which is one of the major components in the extracellular matrix. Hyaluronan can regulate water balance, osmotic pressure, and act as an ion exchange resin. Followed by our recent work on the catalytic reaction mechanism and substrate binding ...

journal_title：Journal of molecular modeling

authors： Li F,Xu D

更新日期：2015-08-01 00:00:00

abstract：:Human gonadotropin hormone receptor, a G-protein coupled receptor, is the target of many medications used in fertility disorders. Obtaining more structural information about the receptor could be useful in many studies related to drug design. In this study, the structure of human gonadotropin receptor was subjected to...

journal_title：Journal of molecular modeling

authors： Sakhteman A,Khoddami M,Negahdaripour M,Mehdizadeh A,Tatar M,Ghasemi Y

更新日期：2016-09-01 00:00:00

abstract：:Various kinetic studies of the addition of hydrogen halides to alkenes were carried out in the 1930s, 1940s, and 1970s. Since then, there have been theoretical analyses of several aspects of alkene reactivity and regioselectivity during hydrohalogenation. A few works have studied the influence of the hydrogen halide w...

journal_title：Journal of molecular modeling

authors： Firme CL

更新日期：2019-04-25 00:00:00

abstract：:A 3D QSAR analysis has been performed on a series of 67 benzodiazepine analogues reported as gamma-secretase inhibitors using molecular field analysis (MFA), with G/PLS to predict steric and electrostatic molecular field interaction for the activity. The MFA study was carried out using a training set of 54 compounds. ...

journal_title：Journal of molecular modeling

authors： Sammi T,Silakari O,Ravikumar M

更新日期：2009-04-01 00:00:00

abstract：:The concepts of polarization (induction), charge transfer and covalent bonding contributions are discussed in terms of weak interactions. They are shown to be different incarnations of the same phenomenon, so that using polarization to describe them is most consistent as it is the only real, measurable and uniquely de...

journal_title：Journal of molecular modeling

authors： Clark T

更新日期：2017-09-27 00:00:00

abstract：:The interaction of a model Lys flanked α-helical peptides K2-X24-K2, (X = A,I,L,L+A,V) with lipid bilayers composed of dimyristoylphosphatidylcholine (DMPC) and dipalmitoylphosphatidylcholine (DPPC) both, in a gel and in a liquid-crystalline state, has been studied by molecular dynamics simulations. It has been shown ...

journal_title：Journal of molecular modeling

authors： Melicherčík M,Holúbeková A,Hianik T,Urban J

更新日期：2013-11-01 00:00:00

abstract：:The heme-AB binding energies (AB = CO, O2) in a wild-type myoglobin (Mb) and two mutants (H64L, V68N) of Mb have been investigated in detail with both DFT and dispersion-corrected DFT methods, where H64L and V68N represent two different, opposite situations. Several dispersion correction approaches were tested in the ...

journal_title：Journal of molecular modeling

authors： Liao MS,Huang MJ,Watts JD

更新日期：2013-08-01 00:00:00

abstract：:Theoretical adiabatic electron affinities are often considered inaccurate because they are referenced to only a single value. Ground state electron affinities for all the main group elements and homonuclear diatomics were identified recently using the normalized binding energy of the hydrogen atom: [0.75420375(3)/2 = ...

journal_title：Journal of molecular modeling

authors： Chen ES,Keith H,Lim T,Pham D,Rosenthal R,Herder C,Pai S,Flores RA,Chen EC

更新日期：2015-04-01 00:00:00

abstract：:The mechanism of C-H bond activation of ethane was catalyzed by palladium halide cations (PdX+ (X = F, Cl, Br, H, and CH3)), which was investigated using density functional theory (DFT) at B3LYP level. The reaction mechanism was taken into account in triplet and singlet spin state potential energy surfaces. For PdF+, ...

journal_title：Journal of molecular modeling

authors： Nie YX,Zhang XX,Yuan YN,Lu F,Geng ZY

更新日期：2020-04-03 00:00:00

abstract：:Fifteen KSP inhibitors were docked into the receptor and the binding mode was analyzed for the first time. It was considered that in addition to the main binding pocket all the inhibitors merged in, there exists a cooperative minor binding pocket, which could be explored for significantly increased binding affinity. I...

journal_title：Journal of molecular modeling

authors： Jiang C,Chen Y,Wang X,You Q

更新日期：2007-09-01 00:00:00

abstract：:Nowadays, scientists are trying to develop low-cost fullerene free acceptors for small organic photovoltaic cells in order to overcome the limitations of fullerene derivatives. Current research work deals with theoretical study on three non-fullerene acceptors based on indaceno, dithiophene core, and thiophene bridge ...

journal_title：Journal of molecular modeling

authors： Ajmal M,Ali U,Javed A,Tariq A,Arif Z,Iqbal J,Shoaib M,Ahmed T

更新日期：2019-09-11 00:00:00

abstract：:The structures of the N-(hydroxymethyl)acetamide (model molecule of ceramide) dimers have been fully optimized at B3LYP/6-311++G** level. The intermolecular hydrogen bonding interaction energies have been calculated using the B3LYP/6-311++G**, B3LYP/6-311++G(2df,2p), MP2(full)/6-311++G** and MP2(full)/6-311++G(2df,2p)...

journal_title：Journal of molecular modeling

authors： Tang HF,Zhong H,Zhang LL,Gong MX,Song SQ,Tian QP

更新日期：2018-05-31 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：:It is well-known that properties of poly(vinyl alcohol) (PVA) in the pure and solution states depend largely on the hydrogen bonding networks formed. In the context of molecular simulation, such networks are handled through the Coulombic interactions. Therefore, a good set of partial atom charges (PACs) for simulation...

journal_title：Journal of molecular modeling

authors： Noorjahan A,Choi P

更新日期：2015-03-01 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：:Matrix metalloproteinase-8 (MMP-8) is the key mediator in initiating type I collagen degradation and is associated with rheumatoid arthritis. In the present study, a pharmacophore hypothesis was developed based on selective non zinc binding inhibitors of MMP-8. The pharmacophore hypothesis was refined manually and val...

journal_title：Journal of molecular modeling

authors： Kalva S,Vinod D,Saleena LM

更新日期：2014-05-01 00:00:00

abstract：:Understanding the interactions of the cage molecules with a variety of invited molecules is getting very important. But, the hydrogen bonds can also play a crucial role in the interaction phenomenon. In this work, natural population analysis (NPA), chemical shifts, and atom in molecules (AIM) analysis have been used t...

journal_title：Journal of molecular modeling

authors： Gassoumi B,Chaabene M,Ghalla H,Chaabane RB

更新日期：2019-12-13 00:00:00

abstract：:Odorant binding proteins (OBPs) are important in insect olfactory recognition. These proteins bind specifically to insect semiochemicals and induce their seeking, mating, and alarm behaviors. Molecular docking and molecular dynamics simulations were performed to provide computational insight into the interaction mode ...

journal_title：Journal of molecular modeling

authors： Wang S,Sun Y,Du S,Qin Y,Duan H,Yang X

更新日期：2016-06-01 00:00:00

abstract：:We design four high performance non-fullerene acceptor materials by applying strong electron withdrawing groups at the end of A-D-A-D-A type organic solar cells molecules and compute their different opto-electronic and photovoltaic properties, including absorption spectrum, electron density, solubility strength, charg...

journal_title：Journal of molecular modeling

authors： Ali U,Javed A,Tallat A,Iqbal J,Raza A

更新日期：2019-01-31 00:00:00

abstract：:Defects in the nanoscale are common in the 2D materials irrespective of the fabricated method. Material performance gets significantly affected due to the presence of defects in 2D materials. In the present study, electronic and mechanical properties of 2D-hexagonal boron nitride (hBN) are investigated. At the electro...

journal_title：Journal of molecular modeling

authors： Sagar TC,Chinthapenta V

更新日期：2020-07-03 00:00:00

abstract：:The interactions between chemosensors, donor-π-acceptor (D-π-A) dipolar organoboron derivatives, and different (CN⁻, F⁻, Cl⁻, and Br⁻) anions have been theoretically investigated using DFT approaches. Theoretical investigations have been performed to explore the optical, electronic, charge transport, and stability pro...

journal_title：Journal of molecular modeling

authors： Jin R,Tang S,Luo D

更新日期：2014-03-01 00:00:00