Identification of novel, less toxic PTP-LAR inhibitors using in silico strategies: pharmacophore modeling, SADMET-based virtual screening and docking.

abstract：:Theoretical and spectroscopic studies of a series of monomeric and dimeric complexes formed through the modification of a zirconium butoxide precursor with acetylacetone and subsequent hydrolysis and/or condensation have been performed by applying DFT/B3LYP/6-31++G(d) and highly accurate RI-ADC(2) methods as well as I...

journal_title：Journal of molecular modeling

authors： Georgieva I,Danchova N,Gutzov S,Trendafilova N

更新日期：2012-06-01 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：:Given the increasing complexity of simulated molecular systems, and the fact that simulation times have now reached milliseconds to seconds, immense amounts of data (in the gigabyte to terabyte range) are produced in current molecular dynamics simulations. Manual analysis of these data is a very time-consuming task, a...

journal_title：Journal of molecular modeling

authors： Victor Paul Raj FR,Exner TE

更新日期：2014-04-01 00:00:00

abstract：:The structures of the 4,4',4″-tris(N,N-phenyl-3-methylphenylamino)triphenylamine (m-MTDATA) molecule and its dimer in their neutral and positively charged forms were studied by performing quantum-chemical calculations at the Hartree-Fock (HF) and density functional theory (DFT) levels of theory using several exchange-...

journal_title：Journal of molecular modeling

authors： Safonov A,Rykova E,Bagaturyants A

更新日期：2018-11-28 00:00:00

abstract：:The behavior of the carbon monoxide (CO) adsorbed on the external surface of H-capped (6,0) zigzag single-walled aluminum nitride nanotube (AlNNT) was studied using parallel and transverse electric field (strengths 0-140 × 10(-4) a.u.) and density functional calculations. The calculated adsorption energies of the CO/A...

journal_title：Journal of molecular modeling

authors： Peyghan AA,Baei MT,Hashemian S,Torabi P

更新日期：2013-02-01 00:00:00

abstract：:The quinolinol derivatives clioquinol (5-chloro-7-iodo-8-quinolinol, Quinoform) and cloxiquine (5-chloro-8-quinolinol) were studied experimentally in the solid state via ³⁵Cl NQR, ¹H-¹⁷O and ¹H-¹⁴N NQDR spectroscopies, and theoretically by density functional theory (DFT). The supramolecular synthon pattern of O-H···N ...

journal_title：Journal of molecular modeling

authors： Latosińska JN,Latosińska M,Tomczak MA,Seliger J,Zagar V

更新日期：2011-07-01 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：:The prediction of the series of complexes [Au(3)Cl(3)M(2)] with M = Li, Na, K, Rb and Cs, has been achieved at the ab initio level of theory. All geometries were fully optimized at the MP2 level of theory; the central Au(3) cluster is capped by chlorine atoms and the alkaline metals lie above and below the plane of th...

journal_title：Journal of molecular modeling

authors： Muñiz J,Sansores LE,Pyykkö P,Martínez A,Salcedo R

更新日期：2009-10-01 00:00:00

abstract：:The impact of a variety of modern computational methods on the structure of biologically relevant zinc complexes is studied. Different density functionals and a Hartree-Fock-based method, scalar-relativistic effects, and basis set integration grid choices, among others, are assessed for set of high-resolution crystall...

journal_title：Journal of molecular modeling

authors： Savasci G,Borges-Martínez M,Berger RJF,Ochsenfeld C,Mera-Adasme R

更新日期：2019-08-09 00:00:00

abstract：:Theoretical studies on 1H-indole-3-acetic acid (IAA) were performed to investigate the conformational properties of dimeric species and vibrational spectra. Experimental infrared spectra at 100 K and 297 K and Raman spectrum at 297 K were analyzed and compared against calculations performed at B3LYP/6-31G** level. A e...

journal_title：Journal of molecular modeling

authors： Lobayan RM,Schmit MC,Jubert AH,Vitale A

更新日期：2011-06-01 00:00:00

abstract：:4-hydroxybenzoate oligoprenyltransferase of E. coli, encoded in the gene ubiA, is an important key enzyme in the biosynthetic pathway to ubiquinone. It catalyzes the prenylation of 4-hydroxybenzoic acid in position 3 using an oligoprenyl diphosphate as a second substrate. Up to now, no X-ray structure of this oligopre...

journal_title：Journal of molecular modeling

authors： Bräuer L,Brandt W,Wessjohann LA

更新日期：2004-12-01 00:00:00

abstract：:Cyclooxygenase (COX) enzymes catalyse the biosynthesis of prostaglandins and thromboxane from arachidonic acid (AA). We summarize in this paper, the development of pharmacophores of a dataset of inhibitors for COX-2 by using the Catalyst/Hypogen module using six chemically diverse series of compounds. Training set con...

journal_title：Journal of molecular modeling

authors： Chopra M,Gupta R,Gupta S,Saluja D

更新日期：2008-11-01 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：:Chemokine receptor 2 (CCR2) is a G-protein coupled receptor (GPCR) and a crucial target for various inflammatory and autoimmune diseases. The structure based antagonists design for many GPCRs, including CCR2, is restricted by the lack of an experimental three dimensional structure. Homology modeling is widely used for...

journal_title：Journal of molecular modeling

authors： Kim JH,Lim JW,Lee SW,Kim K,No KT

更新日期：2011-10-01 00:00:00

abstract：:Geometries and energies of formation of bilirubin formed by reduction of biliverdin via three meso carbon sites, the beta, gamma and delta positions, have been calculated using semiempirical methods. It has been shown that gamma-bilirubin with a ridge-tile conformation forms six intramolecular hydrogen bonds and is th...

journal_title：Journal of molecular modeling

authors： Zahedi M,Kamalipour M,Safari N

更新日期：2002-04-01 00:00:00

abstract：:A theoretical study of a series of five glucose based glycolipid crown ethers and their complexes with Na(+) and K(+) was performed using the density functional theory with B3LYP/6-31 G* to obtain the optimized geometrical structures and electronic properties. The local nucleophilicity of the five molecules was invest...

journal_title：Journal of molecular modeling

authors： Nguan H,Ahmadi S,Hashim R

更新日期：2012-12-01 00:00:00

abstract：:The geometries of three isomers of the C2H4O...2HF tri-molecular heterocyclic hydrogen-bonded complex were examined through B3LYP/aug-cc-pVDZ calculations. Analysis of structural parameters, determination of CHELPG (charge electrostatic potential grid) intermolecular charge transfer, interpretation of infrared stretch...

journal_title：Journal of molecular modeling

authors： de Oliveira BG,Araújo RC,Chagas FF,Carvalho AB,Ramos MN

更新日期：2008-10-01 00:00:00

abstract：:The average pull-out force and interaction energy of polyethylene (PE) cross-linked functionalized carbon nanotubes (cfCNTs) embedded in polymer matrices (PE-cfCNTs@polymers) was studied using molecular dynamics (MD) simulations. Accordingly, the pull-out process of PE-cfCNTs from inside polymer matrices, i.e., Aramid...

journal_title：Journal of molecular modeling

authors： Haghighi S,Ansari R,Ajori S

更新日期：2019-03-29 00:00:00

abstract：:Natural hIFNγ is a glycoprotein with two N-glycosylation sites in each monomer chain, which are independently and differentially glycosylated. Although glycosylation is not necessary for the activity of the cytokine, it was proposed that it protects the cytokine from proteolytic degradation and thus extends its circul...

journal_title：Journal of molecular modeling

authors： Lilkova E,Petkov P,Ilieva N,Krachmarova E,Nacheva G,Litov L

更新日期：2019-04-25 00:00:00

abstract：:The p38-mitogen-activated protein kinases (p38-MAPKs) belong to a family of serine-threonine kinases activated by pro-inflammatory or stressful stimuli that are known to be involved in several diseases. Their biological importance, related to the release of inflammatory pro-cytokines such as tumor necrosis factor-alph...

journal_title：Journal of molecular modeling

authors： Romeiro NC,Albuquerque MG,de Alencastro RB,Ravi M,Hopfinger AJ

更新日期：2006-09-01 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：:Trocarin belongs to group D of prothrombin activators derived from snake venom of Tropidechis carinatus and is a rich non-hepatic source of Xa, the only known hepatic prothrombin activator. The structural and functional similarity with Xa makes trocarin an interesting target for exploring the structure-functional rela...

journal_title：Journal of molecular modeling

authors： Venkateswarlu D,Krishnaswamy S,Darden TA,Pedersen LG

更新日期：2002-10-01 00:00:00

abstract：:The hydrogen bonding interactions between noradrenaline (NA) and DMSO were studied with density functional theory (DFT) regarding their geometries, energies, vibrational frequencies, and topological features of the electron density. The quantum theory of atoms in molecules (QTAIM) and the natural bond orbital (NBO) an...

journal_title：Journal of molecular modeling

authors： Huang Z,Dai Y,Yu L,Wang H

更新日期：2011-10-01 00:00:00

abstract：:Tetrachlorodibenzodioxin (TCDD) is one of the most famous dioxin families that is hazardous to humans and the environment. Designing cheap and novel catalysts for its detecting and removing is an essential need for the environment. In this work, DFT + VdW is used to investigate the potentiality of proposed catalysts i...

journal_title：Journal of molecular modeling

authors： Behjatmanesh-Ardakani R,Heydari A

更新日期：2020-06-03 00:00:00

abstract：:An accurate comparison of the interaction of furan, pyrrole, and thiophene with different gaseous analytes is vital not only for understanding the sensing mechanism of corresponding polymers but also for rational design of new materials. In the present study, DFT calculations at (M05-2X/Aug-cc-PVDZ) have been performe...

journal_title：Journal of molecular modeling

authors： Sajid H,Mahmood T,Ayub K

更新日期：2017-09-26 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：: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：: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：:In this work, a scheme to generate exact wave functions and eigenvalues for the spherically symmetric three-dimensional position-dependent effective mass Schrödinger equation is presented. The methodology is implemented by means of separation of variables and point canonical transformations that allow to recognize a r...

journal_title：Journal of molecular modeling

authors： Ovando G,Morales J,López-Bonilla JL

更新日期：2013-05-01 00:00:00

abstract：:Properties of a new class of hypothetical high-surface-area porous carbons (open carbon frameworks) have been discussed. The limits of hydrogen adsorption in these carbon porous structures have been analyzed in terms of competition between increasing surface accessible for adsorption and the lowering energy of adsorpt...

journal_title：Journal of molecular modeling

authors： Kuchta B,Firlej L,Mohammadhosseini A,Beckner M,Romanos J,Pfeifer P

更新日期：2013-10-01 00:00:00