Structural studies of shikimate dehydrogenase from Bacillus anthracis complexed with cofactor NADP.

abstract：:Ab initio calculations were employed to study the role of ipso carbon hybridization in halogenated compounds RX (R=methyl, phenyl, acetyl, H and X=F, Cl, Br and I) and its interaction with a phosphorus atom, as occurs in the halogen bonded complex type RX⋯PH3. The analysis was performed using ab initio MP2, MP4 and CC...

journal_title：Journal of molecular modeling

authors： Georg HC,Fileti EE,Malaspina T

更新日期：2013-01-01 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 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：:Periplasmic binding proteins are the initial receptors for the transport of various substrates over the inner membrane of gram-negative bacteria. The binding proteins are composed of two domains, and the substrate is entrapped between these domains. For several of the binding proteins it has been established that a cl...

journal_title：Journal of molecular modeling

authors： Siuda I,Thøgersen L

更新日期：2013-11-01 00:00:00

abstract：:Ionic liquids (ILs) have been extensively studied and are considered green solvents capable of replacing traditional organic solvents. In this study, seven 1,2,3-triazolium derivative ILs have been synthesized. In order to study the effect of the cation nature on the ILs cytotoxicity, their structures were first ident...

journal_title：Journal of molecular modeling

authors： Glanzmann N,Carmo AML,Antinarelli LMR,Coimbra ES,Costa LAS,da Silva AD

更新日期：2018-06-14 00:00:00

abstract：:Molecular-dynamics (MD) simulations of urea crystals of different shapes (cubic, rectangular prismatic, and sheet) have been performed using our previously published force field for urea. This force field has been validated by calculating values for the cohesive energy, sublimation temperature, and melting point from ...

journal_title：Journal of molecular modeling

authors： Özpınar GA,Beierlein FR,Peukert W,Zahn D,Clark T

更新日期：2012-08-01 00:00:00

abstract：:We have recently shown that the anti-HIV activities of reverse transcriptase inhibitors can be related quantitatively to properties of the electrostatic potentials on their molecular surfaces. We now introduce the technique of using only segments of the drug molecules in developing such expressions. If an improved cor...

journal_title：Journal of molecular modeling

authors： Brinck T,Jin P,Ma Y,Murray JS,Politzer P

更新日期：2003-04-01 00:00:00

abstract：:In an attempt to analyze structure, function and evolution of HIV-1 GP120 V3, interactions among the Hartree-Fock energy, the conformational entropy and the Shannon entropy were determined for the 1NJ0 set of antibody-bound V3 loop conformers. The Hartree-Fock energy of each conformer was determined at the MINI level ...

journal_title：Journal of molecular modeling

authors： Weltman JK,Skowron G,Loriot GB

更新日期：2006-02-01 00:00:00

abstract：:Here, we report theoretical research into the interaction of the drug tamoxifen drug with tripeptides found in the tumor environment-specifically, asparagine-glycine-arginine (NGR) and arginine-glycine-aspartic acid (RGD). Reactivity parameters of these tripeptides were calculated and their intrinsic reactivities and ...

journal_title：Journal of molecular modeling

authors： Landeros-Martínez LL,Glossman-Mitnik D,Flores-Holguín N

更新日期：2018-11-09 00:00:00

abstract：:The binding properties of the protein-inhibitor complex of human immunodeficiency virus type 1 (HIV-1) protease with the inhibitor TMC-126 are investigated by combining computational alanine scanning (CAS) mutagenesis with binding free-energy decomposition (BFED). The calculated results demonstrate that the flap regio...

journal_title：Journal of molecular modeling

authors： Li D,Han JG,Chen H,Li L,Zhao RN,Liu G,Duan Y

更新日期：2012-05-01 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：: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：:Ab initio calculations were performed to study the quantum chemistry reactions mechanisms among Hg(0), elemental halogen and O3. The geometry of reactions, transition states (TS), intermediates (M) and products were optimized using the MP2 method at the SDD basis function level for Hg, and using 6-311++G (3df, 3pd) fo...

journal_title：Journal of molecular modeling

authors： Gao Z,Lv S,Yang W,Yang P,Ji S,Meng X

更新日期：2015-06-01 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：: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：:A theoretical investigation of the adsorption of CO₂ onto ZrO₂ is presented. Various cluster models were used to mimic different basic and acidic sites on the surface. The method used was the density functional theory with the generalized gradient approximation and including Grimme's empirical model in order to proper...

journal_title：Journal of molecular modeling

authors： Boulet P,Knöfel C,Kuchta B,Hornebecq V,Llewellyn PL

更新日期：2012-11-01 00:00:00

abstract：:DFT calculations were carried out on the homo- and hetero-bimetallic model wires [(η(5)-C5H5)(dpe)Fe-C≡C-C6H4-C≡C-Fe(dpe)(η(5)-C5H5)] (1'), [(η(7)-C7H7)(dpe)Mo-C≡C-C6H4-C≡C-Mo(dpe)(η(7)-C7H7)] (2'), and [(η(5)-C5H5)(dpe)Fe-C≡C-C6H4-C≡C-Mo(dpe)(η(7)-C7H7)] (3') used to tentatively mimic [(η(5)-C5Me5)(dppe)Fe-C≡C-C6H4-C...

journal_title：Journal of molecular modeling

authors： Ladjarafi A,Costuas K,Meghezzi H,Halet JF

更新日期：2015-04-01 00:00:00

abstract：:Metallo-β-lactamases (MβLs) can hydrolyze and deactivate lactam-containing antibiotics, which are the major mechanism to cause drug resistance in the treatment of bacterial infections. This has become a global concern due to the lack of clinically approved inhibitors so far. SMB-1 from Serratia marcescents is a novel ...

journal_title：Journal of molecular modeling

authors： Mu X,Xu D

更新日期：2020-03-07 00:00:00

abstract：:Two uridine 2',3'-cyclic monophosphate (cUMP) derivatives, 5'-deoxy (DcUMP) and 5'-O-methyl (McUMP), were studied by means of quantum chemical methods. Aqueous solvent effects were estimated based on the isodensity-surface polarized-continuum model (IPCM). Gas phase calculations revealed only slight energy differences...

journal_title：Journal of molecular modeling

authors： Grabarkiewicz T,Hoffmann M

更新日期：2006-01-01 00:00:00

abstract：:Herbicides targeting grass plastidic acetyl-CoA carboxylase (ACCase, EC 6.4.1.2) are selectively effective against graminicides. The intensive worldwide use of this herbicide family has selected for resistance genes in a number of grass weed species. Recently, the active-site W374C mutation was found to confer multi-d...

journal_title：Journal of molecular modeling

authors： Zhu XL,Yang WC,Yu NX,Yang SG,Yang GF

更新日期：2011-03-01 00:00:00

abstract：:A computational study has been performed for studying the characteristics of the interaction of phenol with ammonium and methylammonium cations. The effect of the presence of water molecules has also been considered by microhydrating the clusters with up to three water molecules. Clusters of phenol with ammonium and m...

journal_title：Journal of molecular modeling

authors： Rodríguez-Sanz AA,Carrazana-García J,Cabaleiro-Lago EM,Rodríguez-Otero J

更新日期：2013-05-01 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：:Using addition theorems for complete orthonormal sets of exponential type orbitals in the momentum representation introduced by the author, the addition theorems are established for Slater type orbitals in momentum space. With the help of these addition theorems, the general series expansion formulae in terms of the p...

journal_title：Journal of molecular modeling

authors： Guseinov II

更新日期：2005-03-01 00:00:00

abstract：:In this work a molecular modeling study was carried out based on a series of organotin(IV) derivatives which were complexed with ONO-Donor type Schiff base ligands to build up a statistical data pool for researchers. For this purpose, various properties of the selected complexes such as energies, band gaps, chemical r...

journal_title：Journal of molecular modeling

authors： Şirikci G,Ancın NA,Öztaş SG

更新日期：2015-09-01 00:00:00

abstract：:Present theoretical study involves the delta shape complexes of beryllium, magnesium, and calcium where the metal atom interacts perpendicularly with disubstituted acetylene. Most of the complexes are found to be fairly stable. The dependence of second-hyperpolarizability on the basis set with increasing polarization ...

journal_title：Journal of molecular modeling

authors： Hatua K,Nandi PK

更新日期：2015-10-01 00:00:00

abstract：:The influences of the temperature and the BDNPA/BDNPF (A3) content on the mechanical properties of and the binding energies between hexanitrohexaazaisowurtzitane (HNIW) and cellulose acetate butyrate (CAB)/A3 were studied via molecular dynamics simulations. The morphology of HNIW in acetone was simulated using an atta...

journal_title：Journal of molecular modeling

authors： Lan G,Jin S,Wang D,Li J,Lu Z,Jing B,Li L

更新日期：2018-07-02 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：:Human dihydrofolate reductase-like 1 (DHFRL1) has been identified as a second human dihydrofolate reductase (DHFR) enzyme. Although DHFRL1 have high sequence homology with human DHFR, dihydrofolate (DHF) exhibits a lowered binding affinity to DHFRL1 and the corresponding molecular mechanism is still unknown. To addres...

journal_title：Journal of molecular modeling

authors： Gao J,Cui W,Du Y,Ji M

更新日期：2013-12-01 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：: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