Steered molecular dynamics identifies critical residues of the Nodamura virus B2 suppressor of RNAi.

abstract：:The applicability of the newly developed PM6 method for modeling proteins is investigated. In order to allow the geometries of such large systems to be optimized rapidly, three modifications were made to the conventional semiempirical procedure: the matrix algebra method for solving the self-consistent field (SCF) equ...

journal_title：Journal of molecular modeling

authors： Stewart JJ

更新日期：2009-07-01 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

abstract：:This work presents a theoretical study of gallium arsenide (GaAs) nanotubes obtained from the (100), (110) and (111) crystal planes of zincblende structure in order to evaluate the electronic properties. The DFT/B3LYP/6-31G method was used to predict structures and stabilities. It was found that nanotubes from the (11...

journal_title：Journal of molecular modeling

authors： Silva JCF,Dos Santos JD,Taft CA,Martins JBL,Longo E

更新日期：2017-07-01 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：:A density functional theory investigation of adsorption of monomer, dimer and trimer forms of pyrrole on the outer surface of zigzag (7,0) single-walled carbon nanotube (SWCNT) has been reported. Geometries of the complexes were optimized using the M06-2X functional and the 6-31G(d,p) basis set. Moreover, 6-311G(d,p),...

journal_title：Journal of molecular modeling

authors： Shukla MK,Boddu V,Hill F

更新日期：2014-09-01 00:00:00

abstract：:Amino acid sequence alignments of the transcriptional regulator AfeR, which is involved in type 1 quorum sensing (QS) in Acidithiobacillus ferrooxidans bacteria, with other acyl homoserine lactone (AHL)-dependent QS regulators, revealed the presence of strictly or highly conserved residues located in the active site o...

journal_title：Journal of molecular modeling

authors： Soulère L,Guiliani N,Queneau Y,Jerez CA,Doutheau A

更新日期：2008-07-01 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：:Effects of substituents on anion binding in different urea based receptors have been examined using density functional (B3LYP/6-311+G**) level of theory. The complexes formed by a variety of substituted urea with a halide anion (fluoride) and an oxy-anion (acetate) have been calculated. The stronger complexes were pre...

journal_title：Journal of molecular modeling

authors： Ghosh A,Jose DA,Das A,Ganguly B

更新日期：2010-09-01 00:00:00

abstract：:The formation of selenium species in some biological processes involves the generation of ionic and radical intermediates such as RSe●, RSe-, RSeO●, and RSeO-, among others. We performed a theoretical study of the possible mechanisms for the reaction of the two simplest Se radicals-the hydroselenyl (HSe●) and seleneni...

journal_title：Journal of molecular modeling

authors： Vega-Teijido MA,Kieninger M,Ventura ON

更新日期：2017-12-05 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：:In this paper, coupled cluster methods CC2, CCSD, CCSDR(3) and EOM-CCSD(T) have been benchmarked against CC3 for the transition energies of nucleobases. Beside presenting vertical excitation energies for about 30 singlet transitions of four molecules, the results are analyzed statistically and problematic cases have b...

journal_title：Journal of molecular modeling

authors： Kánnár D,Szalay PG

更新日期：2014-11-01 00:00:00

abstract：:Paracetamol is a relatively safe analgesia/antipyretic drug without the risks of addiction, dependence, tolerance, and withdrawal when used alone. However, when administrated in an opioid/paracetamol combination product, which often contains a large quantity of paracetamol, it can be potentially dangerous due to the r...

journal_title：Journal of molecular modeling

authors： Wang Y,Lin W,Wu N,He X,Wang J,Feng Z,Xie XQ

更新日期：2018-08-18 00:00:00

abstract：:Through the B3LYP/6-311++G(d,p) calculations, theoretical studies of structural parameters, electronic properties, infrared vibration modes, and charge density topologies on the C2H4O∙∙∙HX and C2H5N∙∙∙HX (X = F or O-F) heterocylic hydrogen complexes are presented. The H-bond distances and high energies point out stron...

journal_title：Journal of molecular modeling

authors： Oliveira BG

更新日期：2015-11-01 00:00:00

abstract：:The binding geometry of fluorouracil/cucurbit[n]urils (CB[n]s) complexes with n = 5-8 is investigated using the first-principles van der Waals density functional (vdW-DF) method, involving full geometry optimization. Such host-guest complexes are typically calculated using conventional DFT method, which significantly ...

journal_title：Journal of molecular modeling

authors： Sabet M,Ganji MD

更新日期：2013-09-01 00:00:00

abstract：:We present a critical discussion related to the recent definition of the intrinsic reactivity index, IRI, (Tetrahedron Lett. 2013, 54, 339-342; Tetrahedron 2013, 69, 4247-4258) formulated to describe both, electrophilicity (charge acceptance) and nucleophilicity (charge donation) reactivities. We here stress that such...

journal_title：Journal of molecular modeling

authors： Chamorro E,Melin J

更新日期：2015-03-01 00:00:00

abstract：:Iridium (III) 2-phenylpyridine (ppy) complexes with two suitable monodentate L ligands [Ir(ppy)₂(L)₂]⁺ (ppy = 2-phenylpyridine, py = pyridine, L = 4-pyCN 1, 4-pyCHO 2, 4-pyCl 3, py 4, 4-pyNH₂ 5) were studied by density functional theory (DFT) and time-dependent DFT methods. The influences of ligands L on the electroni...

journal_title：Journal of molecular modeling

authors： Zhang TT,Qi XX,Jia J,Wu HS

更新日期：2012-10-01 00:00:00

abstract：:The effect of terminal GLY114* deletion on the binding affinity of the PA-IIL lectin toward L: -fucose was investigated. Both experimental (isothermal titration calorimetry) and computational (molecular dynamics simulations) methods have shown that the deletion mutation decreases the L-fucose affinity. It implies that...

journal_title：Journal of molecular modeling

authors： Wimmerová M,Mishra NK,Pokorná M,Koca J

更新日期：2009-06-01 00:00:00

abstract：:We present a theoretical study of the adsorption of 2,2,6,6-tetramethylpiperidine-1-oxoammonium cation (TEMPO) onto the TiO₂(110) surface rutile, investigating its bonding nature, electron properties and structural stability. Based on the results obtained with the PBE0/def2-SVP method, natural bond orbital (NBO) analy...

journal_title：Journal of molecular modeling

authors： Nieto-López I,Hernández-García L,Bonilla-Cruz J,Sanchez M

更新日期：2014-03-01 00:00:00

abstract：:Recent ab initio investigations of some complexes formed between carbon dioxide and its analogues carbonyl sulfide, carbonyl selenide, carbon disulfide, and thiocarbonyl selenide and the common bases ammonia, water, phosphine, and hydrogen sulfide have revealed significant differences between the properties of those c...

journal_title：Journal of molecular modeling

authors： Ramasami P,Ford TA

更新日期：2015-02-01 00:00:00

abstract：:The structural and energetic properties of native and oxidized telomeric complexes were defined by means of molecular dynamic (MD) simulations. As a starting point, the experimental conformation of B-DNA d(GpTpTpApGpGpGpTpTpApGpGpG) oligomer bound to human protein telomeric repeat binding factor 1 (TRF1) was used. The...

journal_title：Journal of molecular modeling

authors： Czeleń P,Cysewski P

更新日期：2013-08-01 00:00:00

abstract：:The distinguishing property of Sm protein associations is very high stability. In order to understand this property, we analyzed the interfaces and compared the properties of Sm protein interfaces with those of a test set, the Binding Interface Database (BID). The comparison revealed that the main differences between ...

journal_title：Journal of molecular modeling

authors： Stojanović SD,Zarić BL,Zarić SD

更新日期：2010-11-01 00:00:00

abstract：:The dopamine (DAT), serotontin (SERT) and noradrenalin (NET) transporters are molecular targets for different classes of psychotropic drugs. The crystal structure of Aquifex aeolicus LeuT(Aa) was used as a template for molecular modeling of DAT, SERT and NET, and two putative drug binding sites (pocket 1 and 2) in eac...

journal_title：Journal of molecular modeling

authors： Ravna AW,Sylte I,Dahl SG

更新日期：2009-10-01 00:00:00

abstract：:Aluminum enriched 1, 1-diamino-2, 2-dinitroethylene (Al-FOX-7) crystal, as a new high energy density material (HEDM), was designed and investigated using grand canonical monte carlo (GCMC), NVT+NPT-molecular dynamics (MD) and GGA-PBE-density functional theory (DFT) methods. The results show that, Al atoms break out H-...

journal_title：Journal of molecular modeling

authors： Bian L,Shu Y,Xu J,Wang L

更新日期：2013-01-01 00:00:00

abstract：:Fully atomistic molecular dynamics simulation studies of thermotropic bilayers were performed using a set of glycosides namely n-octyl-β-D-glucopyranoside (β-C8Glc), n-octyl-α-D-glucopyranoside (α-C8Glc), n-octyl-β-D-galactopyranoside (β-C8Gal), and n-octyl-α-D-galactopyranoside (α-C8Gal) to investigate the stereochem...

journal_title：Journal of molecular modeling

authors： Ahmadi S,Manickam Achari V,Nguan H,Hashim R

更新日期：2014-03-01 00:00:00

abstract：:The structure of a two-dimensional film formed by adsorbed polymer chains was studied by means of Monte Carlo simulations. The polymer chains were represented by linear sequences of lattice beads and positions of these beads were restricted to vertices of a two-dimensional square lattice. Two different Monte Carlo met...

journal_title：Journal of molecular modeling

authors： Pawłowska M,Sikorski A

更新日期：2013-10-01 00:00:00

abstract：:The pathogen Legionella longbeachae is a causative agent of legionellosis. The antibiotic resistance is the major problem of this modern world. Thus, selective pressure warrants the need for identification of newer drug target. In current study, subtractive proteomics approach screen out SIS (sugar isomerase) domain p...

journal_title：Journal of molecular modeling

authors： Ahmad F,Shabaz Z,Azam SS

更新日期：2020-08-03 00:00:00

abstract：:The internal rotation in ammonia borane (AB) was studied on the basis of natural orbitals for chemical valence (NOCV) and eigenvectors for Pauli repulsion (NOPR). We found that the total hyperconjugation stabilization (ca. 5 kcal mol(-1)), based on the charge transfer from the occupied σ (B-H) orbitals into the empty ...

journal_title：Journal of molecular modeling

authors： Parafiniuk M,Mitoraj MP

更新日期：2014-06-01 00:00:00

abstract：:5-Nitro-3-trinitromethyl-1H-1,2,4-triazole (NTMT, A) and its substituted derivatives A-CH3, A-OCH3, A-NH2, A-OH, A-NO2, and A-ONO2 were studied using density functional theory (DFT). For all of the molecules except for A-ONO2, the C-NO2 bond in the trinitromethyl group was found to be the weakest, and no transition st...

journal_title：Journal of molecular modeling

authors： Zhang X,Gong X

更新日期：2015-02-01 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：: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