Solvent accessible surface area approximations for rapid and accurate protein structure prediction.

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：:G-Quadruplex and i-Motif-forming sequences in the promoter regions of several oncogenes show promise as targets for the regulation of oncogenes. In this study, molecular models were created for the c-MYC NHE-III(1) (nuclease hypersensitivity element III(1)) from two 39-base complementary sequences. The NHE modeled her...

journal_title：Journal of molecular modeling

authors： Cashman DJ,Buscaglia R,Freyer MW,Dettler J,Hurley LH,Lewis EA

更新日期：2008-02-01 00:00:00

abstract：:Understanding the structure and properties at the electrolyte-electrode interface is vital for the rational design of the supercapacitors or other electrochemical devices. In this work, we explored the influence of interlayer spacing of the MoS2 electrode on the interfacial structure and electrical properties of sodiu...

journal_title：Journal of molecular modeling

authors： Wang M,Wang Y,Li M,Wang S,He H

更新日期：2021-01-18 00:00:00

abstract：:Multi-tetrazole derivatives with conjugated structures were designed and investigated in this study. Using quantum chemistry methods, the crystal structures, electrostatic potentials (ESPs), multicenter bond orders, HOMO-LUMO energy gaps, and detonation properties of the derivatives were calculated. As expected, these...

journal_title：Journal of molecular modeling

authors： Sun S,Lu M

更新日期：2018-06-23 00:00:00

abstract：:The structural characteristics involving thermal stabilities of liquid nitromethane (NM)—one of the simplest energetic materials—confined within a graphene (GRA) bilayer were investigated by means of all-atom molecular dynamics simulations and density functional theory calculations. The results show that ordered and l...

journal_title：Journal of molecular modeling

authors： Liu Y,Yu T,Lai W,Kang Y,Ge Z

更新日期：2015-03-01 00:00:00

abstract：:Using ligand and receptor based virtual screening approaches we have identified potential virtual screening hits targeting type II dehydroquinase from Mycobacterium tuberculosis, an effective and validated anti-mycobacterial target. Initially, we applied a virtual screening workflow based on a combination of 2D struct...

journal_title：Journal of molecular modeling

authors： Kumar A,Siddiqi MI,Miertus S

更新日期：2010-04-01 00:00:00

abstract：:The structural parameters, Raman/IR spectra, and vibrational and thermodynamic properties of α-RDX and γ-RDX were investigated by performing first-principles calculations using the CASTEP program. The obtained structural parameters and vibrational frequencies of the internal modes of α-RDX are consistent with previous...

journal_title：Journal of molecular modeling

authors： Zhu SH,Qin H,Zeng W,Cai YM,Jin XY,Wang YH,Liu FS,Tang B,Liu QJ

更新日期：2019-06-07 00:00:00

abstract：:APUAMA is a free software designed to determine the reaction rate and thermodynamic properties of chemical species of a reagent system. With data from electronic structure calculations, the APUAMA determine the rate constant with tunneling correction, such as Wigner, Eckart and small curvature, and also, include the r...

journal_title：Journal of molecular modeling

authors： Euclides HO,P Barreto PR

更新日期：2017-06-01 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：:3-phosphoinositide-dependent protein kinase-1 (PDK1) plays a crucial role in the signal transduction of massive growth-related protein kinases. In this work, a computational study has been performed to investigate the binding pose of the hydrolyzed product of SBF1 (SBF1-) with PDK1. The binding pose was predicted by V...

journal_title：Journal of molecular modeling

authors： Liu W,Li P,Mei Y

更新日期：2019-06-13 00:00:00

abstract：:NBO-NJC decomposition of vicinal (3)J HH spin-spin coupling constants into Lewis, delocalization, and repolarization contributions are presented. A deep study allows to assign the main contributions to specific orbitals or electron delocalizations between two orbitals. (3)J HH torsional dependence and the substituent ...

journal_title：Journal of molecular modeling

authors： García de la Vega JM,San Fabián J

更新日期：2014-07-01 00:00:00

abstract：:Density functional theory (DFT) was used to investigate cobalt(0)-catalyzed intramolecular hydroacylation of 4-pentenal. The calculated results indicated the involvement of five possible reaction pathways: the formation of cyclopentanone, cyclobutanone, butylenes, cyclobutane, and cyclopropane, respectively. The forme...

journal_title：Journal of molecular modeling

authors： Meng Q,Wang F,Li M

更新日期：2013-06-01 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 double-histone fold is a rare protein fold in which two consecutive regions characterized by the typical structure of histones assemble together, thus giving a histone pseudodimer. Previously, this fold was found in a few prokaryotic histones and in the regulatory region of guanine-nucleotide exchange factors of t...

journal_title：Journal of molecular modeling

authors： Greco C,Sacco E,Vanoni M,De Gioia L

更新日期：2005-12-01 00:00:00

abstract：:This work focuses on the role of the dynamic hydrogen bonds (HB) formed in an aqueous solution of aspirin using molecular dynamics simulation. The statistics reveal the existence of internal HB that inhibit the rotational movements of the acetyl and the carboxylic acid groups, forcing the molecule to adopt a closed co...

journal_title：Journal of molecular modeling

authors： Donnamaria MC,de Xammar Oro JR

更新日期：2011-10-01 00:00:00

abstract：:Understanding the interaction between graphene and polymers is of essential interest when designing novel nanocomposites with reinforced mechanical and electrical properties. In this computational study, the interaction of pristine graphene (PG) and graphene oxide (GO) with a series of functional groups, representativ...

journal_title：Journal of molecular modeling

authors： Güryel S,Alonso M,Hajgató B,Dauphin Y,Van Lier G,Geerlings P,De Proft F

更新日期：2017-02-01 00:00:00

abstract：:The three-dimensional (3D) structure of the substrate binding domain (SBD) of human ubiquitin ligase Siah2 (seven in absentia homolog) was constructed based on the homology modeling approach using the Modeller 9v7 program. The molecular dynamics method was utilized to refine the model and it was further assessed by Pr...

journal_title：Journal of molecular modeling

authors： Anupriya G,Roopa K,Basappa S,Chong YS,Annamalai L

更新日期：2011-12-01 00:00:00

abstract：:The ladder-type polyheterofluorenes were investigated theoretically by using density functional theory (DFT) to reveal their optical and electronic properties for applications in organic optoelectronic devices. The incorporation of heteroatoms (B, Si, Ge, N, P, O, and S) into the ladder-type highly fused polyfluorene ...

journal_title：Journal of molecular modeling

authors： Zheng C,Tao Y,Cao JZ,Chen RF,Zhao P,Wu XJ,Huang W

更新日期：2012-11-01 00:00:00

abstract：:The nature of E-M bonds in CpE-MCp (E = B, Al, Ga; M = Li, Na, K; Cp = η (5)-C5H5) donor-acceptor sandwiches was studied using the atoms in molecules (AIM) theory, electron localization function (ELF), energy decomposition analysis (EDA), and natural bond orbital analysis (NBO) methods. Both topological and orbital an...

journal_title：Journal of molecular modeling

authors： Huo S,Meng D,Zhang X,Meng L,Li X

更新日期：2014-10-01 00:00:00

abstract：:In this study, the newly synthesized non-centrosymmetric, 4-dimethylamino-3'-isothiocyanatochalcone (PKA) compound was presented. This compound belongs to the chalcone group, and its main purpose is to be used in biomedical imaging as a fluorescence dye. For this reason, the linear and nonlinear properties in solvents...

journal_title：Journal of molecular modeling

authors： Krawczyk P,Pietrzak M,Janek T,Jędrzejewska B,Cysewski P

更新日期：2016-06-01 00:00:00

abstract：:Corynebacterium pseudotuberculosis is a facultatively intracellular Gram-positive bacterium that causes caseous lymphadenitis, principally in sheep and goats, though sometimes in other species of animals, leading to considerable economic losses. This pathogen has a TCS known as PhoPR, which consists of a sensory histi...

journal_title：Journal of molecular modeling

authors： Moraes G,Azevedo V,Costa M,Miyoshi A,Silva A,da Silva V,de Oliveira D,Teixeira MF,Lameira J,Alves CN

更新日期：2012-03-01 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：:The contribution of folic acid (FA)-tryptophan interactions to FA-protein association was investigated in the context of using FA as a drug carrier in protein delivery systems. Bovine serum albumin (BSA) and indolicidin were used as model proteins in the study. The FA-BSA complex was characterized by using the Bradfor...

journal_title：Journal of molecular modeling

authors： Gupta R,Kalita P,Patil O,Mohanty S

更新日期：2015-12-01 00:00:00

abstract：:We report results of numerical simulations of complex fluids, using a combination of discrete-particle methods. Our molecular modeling repertoire comprises three simulation techniques: molecular dynamics (MD), dissipative particle dynamics (DPD), and the fluid particle model (FPM). This type of model can depict multi-...

journal_title：Journal of molecular modeling

authors： Dzwinel W,Yuen DA,Boryczko K

更新日期：2002-01-01 00:00:00

abstract：:The design of stable and inexpensive artificial enzymes with potent catalytic activity is a growing field in peptide science. The first step in this design process is to understand the key factors that can affect the conformational preference of an enzyme and correlate them with its catalytic activity. In this work, m...

journal_title：Journal of molecular modeling

authors： Honarparvar B,Skelton AA

更新日期：2015-04-01 00:00:00

abstract：:The drug discovery process typically involves target identification and design of suitable drug molecules against these targets. Despite decades of experimental investigations in the drug discovery domain, about 96% overall failure rate has been recorded in drug development due to the "undruggability" of various ident...

journal_title：Journal of molecular modeling

authors： Agoni C,Olotu FA,Ramharack P,Soliman ME

更新日期：2020-05-08 00:00:00

abstract：:A series of no-chlorine and oxygen-rich hydrazine derivatives (hydrazine modified with -NO₂ and NO₃(-) groups) was designed and optimized to obtain molecular geometries and electronic structures at density functional theory-B3PW91/6-311++G(3df,3pd) level. Some important properties such as bond dissociation enthalpy, d...

journal_title：Journal of molecular modeling

authors： Wang PC,Zhu ZS,Xu J,Zhao XJ,Lu M

更新日期：2013-06-01 00:00:00

abstract：:Prussian Blue is a paradigmatic mixed valence material and a parent compound to a broad family of electronically, optically, and magnetically active materials. Its exact composition varies greatly depending on the preparation route, leading to large variations in its electronic properties. The influence of water molec...

journal_title：Journal of molecular modeling

authors： Wojdeł JC

更新日期：2009-06-01 00:00:00

abstract：:Detailed density functional theory (DFT) calculations on the structure and harmonic frequencies of model all-trans and all-cis polyenes were undertaken. For the first time, we report on the convergence of selected B3LYP/6-311++G** and BLYP/6-311++G** calculated structural parameters resulting from a systematic increas...

journal_title：Journal of molecular modeling

authors： Kupka T,Buczek A,Broda MA,Stachów M,Tarnowski P

更新日期：2016-05-01 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