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Journal of Molecular Graphics & Modelling

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https://www.readbyqxmd.com/read/28214629/effects-of-metal-ion-replacement-on-pyrazinamidase-activity-a-quantum-mechanical-study
#1
Mahmoud Khadem-Maaref, Faramarz Mehrnejad, Arash Phirouznia
Pyrazinamidase (PZase), a metalloenzyme, is responsible for acidic modification of pyrazinamide (PZA), a drug used in tuberculosis treatment. The metal coordination site of the enzyme is able to coordinate various divalent metal cofactors. Previous experimental studies have demonstrated that metal ions, such as Co(2+), Mn(2+), and Zn(2+), are able to reactivate metal-depleted PZase, while others including Cu(2+), Fe(2+), and Mg(2+), cannot restore activity. In this study, we investigated binding of various metal ions to the metal coordination site (MCS) of the enzyme using quantum mechanical calculations...
February 2, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28182995/exploring-the-possibility-to-store-the-mixed-oxygen-hydrogen-cluster-in-clathrate-hydrate-in-molar-ratio-1-2-o2-2h2
#2
Yan Qin, Qi-Shi Du, Neng-Zhong Xie, Jian-Xiu Li, Ri-Bo Huang
An interesting possibility is explored: storing the mixture of oxygen and hydrogen in clathrate hydrate in molar ratio 1:2. The interaction energies between oxygen, hydrogen, and clathrate hydrate are calculated using high level quantum chemical methods. The useful conclusion points from this study are summarized as follows. (1) The interaction energies of oxygen-hydrogen mixed cluster are larger than the energies of pure hydrogen molecular cluster. (2) The affinity of oxygen molecules with water molecules is larger than that of the hydrogen molecules with water molecules...
February 1, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28214437/chempreview-an-augmented-reality-based-molecular-interface
#3
Min Zheng, Mark P Waller
Human computer interfaces make computational science more comprehensible and impactful. Complex 3D structures such as proteins or DNA are magnified by digital representations and displayed on two-dimensional monitors. Augmented reality has recently opened another door to access the virtual three-dimensional world. Herein, we present an augmented reality application called ChemPreview with the potential to manipulate bio-molecular structures at an atomistic level. ChemPreview is available at https://github.com/wallerlab/chem-preview/releases, and is built on top of the Meta 1 platform https://www...
January 31, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28226271/thermal-buckling-behavior-of-defective-cnts-under-pre-load-a-molecular-dynamics-study
#4
Fahimeh Mehralian, Yaghoub Tadi Beni, Yaser Kiani
Current study is concentrated on the extraordinary properties of defective carbon nanotubes (CNTs). The role of vacancy defects in thermal buckling response of precompressed CNTs is explored via molecular dynamics (MD) simulations. Defective CNTs are initially compressed at a certain ratio of their critical buckling strain and then undergo a uniform temperature rise. Comprehensive study is implemented on both armchair and zigzag CNTs with different vacancy defects including monovacancy, symmetric bivacancy and asymmetric bivacancy...
January 25, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28129595/3d-sdar-modeling-of-herg-potassium-channel-affinity-a-case-study-in-model-design-and-toxicophore-identification
#5
Iva B Stoyanova-Slavova, Svetoslav H Slavov, Dan A Buzatu, Richard D Beger, Jon G Wilkes
A dataset of 237 human Ether-à-go-go Related Gene (hERG) potassium channel inhibitors (180 of which were used for model building and validation, whereas 57 constituted the "true" external prediction set) collected from 22 literature sources was modeled by 3D-SDAR. To produce reliable and reproducible classification models for hERG blocking, the initial set of 180 chemicals was split into two subsets: a balanced modeling set consisting of 118 compounds and an unbalanced validation set comprised of 62 compounds...
January 16, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28129593/multi-step-virtual-screening-to-develop-selective-dyrk1a-inhibitors
#6
Tomoko Koyama, Noriyuki Yamaotsu, Izumi Nakagome, Shin-Ichiro Ozawa, Tomoki Yoshida, Daichi Hayakawa, Shuichi Hirono
Developing selective inhibitors for a particular kinase remains a major challenge in kinase-targeted drug discovery. Here we performed a multi-step virtual screening for dual-specificity tyrosine-phosphorylation-regulated kinase 1A (DYRK1A) inhibitors by focusing on the selectivity for DYRK1A over cyclin-dependent kinase 5 (CDK5). To examine the key factors contributing to the selectivity, we constructed logistic regression models to discriminate between actives and inactives for DYRK1A and CDK5, respectively, using residue-based binding free energies...
January 15, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28129592/prediction-of-enthalpies-of-sublimation-of-high-nitrogen-energetic-compounds-modified-politzer-model
#7
Marina A Suntsova, Olga V Dorofeeva
In the framework of the Politzer approach, the improved electrostatic potential model for estimating enthalpies of sublimation of nitrogen-rich energetic compounds is proposed on the basis of reliable experimental enthalpies of sublimation for 185 compounds. The accuracy of predicted values is estimated to be within ±20kJ/mol. The model was applied to estimate the solid phase enthalpies of formation of some tetrazole-, tetrazine-, furazan-, and furoxan-based energetic compounds.
January 11, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28129594/importance-of-hydrogen-bonding-and-aromaticity-indices-in-qsar-modeling-of-the-antioxidative-capacity-of-selected-poly-phenolic-antioxidants
#8
Svetlana Jeremić, Slavko Radenković, Miloš Filipović, Marija Antić, Ana Amić, Zoran Marković
The quantitative structure-activity relationship (QSAR) models for predicting antioxidative capacity of 21 structurally similar natural and synthetic phenolic antioxidants was considered. The one-, two- and three-descriptor QSAR models were developed. For this purpose the literature data on the vitamin C equivalent antioxidative capacity (VCEAC) values were used as experimental descriptor of antioxidative capacity. Some thermodynamic and aromaticity properties, as well as the natural bond analysis (NBO) based quantities aimed at measuring the strength of intramolecular hydrogen bonds, were used as independent variables...
January 10, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28110183/noncovalent-interaction-assisted-fullerene-for-the-transportation-of-some-brain-anticancer-drugs-a-theoretical-study
#9
Pabitra Narayan Samanta, Kalyan Kumar Das
The treatment of brain cancer like glioblastoma multiforme often uses chemotherapeutic drugs like temozolomide, procarbazine, carmustine, and lomustine. Fullerene loaded with these drugs help to cross the blood brain barriers. The adsorptions of the four drug molecules on the surface of the fullerene are studied mostly by using density functional theory (DFT) based method at the M06-2X/6-31G(d) level of calculations. In all four cases, the estimated interactions are noncovalent type and the average adsorption energy lies in between -5 and -11kcal/mol in the gas phase...
January 8, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28092830/trpv1-antagonism-by-piperazinyl-aryl-compounds-a-topomer-comfa-study-and-its-use-in-virtual-screening-for-identification-of-novel-antagonists
#10
Rajendra Kristam, Shashidhar N Rao, Anne Sudha D'Cruz, Vijayalakshmi Mahadevan, Vellarkad N Viswanadhan
Transient Receptor Potential Vanilloid, member 1 (TRPV1), is a non-selective cation channel belonging to the transient receptor potential (TRP) family of ion channels. It occurs in the peripheral and central nervous system, activated by a variety of exogenous and endogenous stimuli, thus playing a key role in transmission of pain. This has been a target for chronic pain since more than a decade and a number of antagonists that progressed into clinical trials have failed due to the unexpected side effect of core body temperature rise, thus halting progress in this field...
January 7, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28167312/first-protein-drug-target-s-appraisal-of-lead-likeness-descriptors-to-unfold-the-intervening-chemical-space
#11
Mohd Athar, Mohsin Y Lone, Prakash C Jha
Despite the advances in combinatorial chemistry, high throughput and virtual screening experiments, plethora of clinical studies disquiet due to lead and drug-likeness attritions. For mitigation, the knowledge of physicochemical properties are really useful for guiding and selection of compounds from libraries dictated by certain rule of thumbs. However, robust bio-technological and instrumental innovations have created exponential increase in novel compounds and databases which compelled rethinking of the evaluation procedures...
January 6, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28135672/binary-classification-of-imbalanced-datasets-using-conformal-prediction
#12
Ulf Norinder, Scott Boyer
Aggregated Conformal Prediction is used as an effective alternative to other, more complicated and/or ambiguous methods involving various balancing measures when modelling severely imbalanced datasets. Additional explicit balancing measures other than those already apart of the Conformal Prediction framework are shown not to be required. The Aggregated Conformal Prediction procedure appears to be a promising approach for severely imbalanced datasets in order to retrieve a large majority of active minority class compounds while avoiding information loss or distortion...
January 6, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28110184/structural-analysis-of-binding-functionality-of-folic-acid-peg-dendrimers-against-folate-receptor
#13
Diana Sampogna-Mireles, Ingrid D Araya-Durán, Valeria Márquez-Miranda, Jesús A Valencia-Gallegos, Fernando D González-Nilo
Dendrimers functionalized with folic acid (FA) are drug delivery systems that can selectively target cancer cells with folate receptors (FR-α) overexpression. Incorporation of polyethylene glycol (PEG) can enhance dendrimers solubility and pharmacokinetics, but ligand-receptor binding must not be affected. In this work we characterized, at atomic level, the binding functionality of conventional site-specific dendrimers conjugated with FA with PEG 750 or PEG 3350 as a linker. After Molecular Dynamics simulation, we observed that both PEG's did not interfere over ligand-receptor binding functionality...
January 6, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28092835/effects-of-the-central-potassium-ions-on-the-g-quadruplex-and-stabilizer-binding
#14
Zhiguo Wang, Jun-Ping Liu
Human telomeres undertake the structure of intra-molecular parallel G-quadruplex in the presence of K(+) in eukaryotic cell. Stabilization of the telomere G-quadruplex represents a potential strategy to prevent telomere lengthening by telomerase in cancer therapy. Current work demonstrates that the binding of central K(+) with the parallel G-quadruplex is a coordinated water directed step-wise process. The K(+) above the top G-tetrad is prone to leak into environment and the 5'-adenine quickly flips over the top G-tetrad, leading to the bottom gate of G-tetrads as the only viable pathway of K(+) binding...
January 6, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28092834/computational-exploration-of-regioselectivity-and-atmospheric-lifetime-in-no3-initiated-reactions-of-ch3och3-and-ch3och2ch3
#15
Jin-Ting Ye, Feng-Yang Bai, Shao-Qing Shi, Xiu-Mei Pan
The NO3-initiated reactions of CH3OCH3 and CH3OCH2CH3 have been investigated by the BHandHLYP method in conjunction with the 6-311G(d,p) basis set. Thermodynamic and kinetic data are further refined using the comparatively accurate CCSD(T) method. According to the values of reaction enthalpies (ΔHr,298(θ)) and reaction Gibbs free energies (ΔGr,298(θ)) from CH3OCH2CH3 with NO3 system, we find that H-abstraction pathway from the α-CH2 group is more exothermic. It is further confirmed by the calculated CH bond dissociation energy of CH3OCH2CH3 molecule...
January 6, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28110185/computational-analysis-of-amsacrine-resistance-in-human-topoisomerase-ii-alpha-mutants-r487k-and-e571k-using-homology-modeling-docking-and-all-atom-molecular-dynamics-simulation-in-explicit-solvent
#16
Safaa Sader, Chun Wu
Amsacrine is an effective topoisomerase II enzyme inhibitor in acute lymphatic leukemia. Previous experimental studies have successfully identified two important mutations (R487K and E571K) conferring 100 and 25 fold resistance to Amsacrine respectively. Although the reduction of the cleavage ligand-DNA-protein ternary complex has been well thought as the major cause of drug resistance, the detailed energetic, structural and dynamic mechanisms remain to be elusive. In this study, we constructed human topoisomerase II alpha (hTop2α) homology model docked with Amsacrine based on crystal structure of human Top2β in complex with etoposide...
January 4, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28107751/molecular-modeling-study-of-cp-690550-derivatives-as-jak3-kinase-inhibitors-through-combined-3d-qsar-molecular-docking-and-dynamics-simulation-techniques
#17
Jing Li Wang, Li Ping Cheng, Tian Chi Wang, Wei Deng, Fan Hong Wu
To develop more potent JAK3 kinase inhibitors, a series of CP-690550 derivatives were investigated using combined molecular modeling techniques, such as 3D-QSAR, molecular docking and molecular dynamics (MD). The leave-one-out correlation (q(2)) and non-cross-validated correlation coefficient (r(2)) of the best CoMFA model are 0.715 and 0.992, respectively. The q(2) and r(2) values of the best CoMSIA model are 0.739 and 0.995, respectively. The steric, electrostatic, and hydrophobic fields played important roles in determining the inhibitory activity of CP-690550 derivatives...
January 4, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28092829/enhancing-4-propylheptane-dissociation-with-nickel-nanocluster-based-on-molecular-dynamics-simulations
#18
Margarita G Ilyina, Edward M Khamitov, Rail N Galiakhmetov, Ildar A Mustafin, Akhat G Mustafin
In the present work, a 0.4nm nickel cluster has been theoretically studied. Its equilibrium structural parameters have been calculated by the DFT method based on the PBEH1PBE hybrid functional and split-valence basis set Lanl2DZ including effective core potentials. We have systematically considered diverse spin states of this cluster and find out its ground state. The relative stability of these states depends on the HOMO-LUMO gap. The interaction of the Ni6 with 4-propylheptane С10Н22 has been studied to simulate the process of catalytic cracking of hydrocarbons...
January 3, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28092836/antiviral-drug-acyclovir-exhibits-antitumor-activity-via-targeting-%C3%AE-trcp1-molecular-docking-and-dynamics-simulation-study
#19
Shagufta Shafique, Sajid Rashid
The critical role of βTrCP1 in cancer development makes it a discerning target for the development of small drug like molecules. Currently, no inhibitor exists that is able to target its substrate binding site. Through molecular docking and dynamics simulation assays, we explored the comparative binding pattern of βTrCP1-WD40 domain with ACV and its phospho-derivatives (ACVMP, ACVDP and ACVTP). Consequently, through principal component analysis, βTrCP1-ACVTP was found to be more stable complex by obscuring a reduced conformational space than other systems...
December 31, 2016: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28092833/study-of-molecular-interactions-between-chitosan-and-vi-antigen
#20
Natália de Farias Silva, Raimundo Lopes da Silva, Kalene de Oliveira Almeida, Antônio Edilson Sousa do Nascimento-Júnior, Davi do Socorro Barros Brasil, José Otávio Carréra Silva-Júnior, Francisco Martins Teixeira, Roseane Maria Ribeiro-Costa
Chitosan has attracted much interest due to its special physical and chemical properties related to drug administration. Nanoparticles delivery systems from Vi Antigen are a promising approach in the struggle against typhoid fever. In this paper, we reported the obtainment and the characterization of Vi Antigen by Infrared spectroscopy as well as Molecular Modeling and Computational Chemistry studies of the Chitosan-Vi Antigen interaction through theoretical models. The results of the theoretical and experimental Infrared spectroscopy showed important bands related to N-Acetyl and O-Acetyl groups present in Vi Antigen...
December 31, 2016: Journal of Molecular Graphics & Modelling
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