Cryo-EM density map fitting driven in-silico structure of human soluble guanylate cyclase (hsGC) reveals functional aspects of inter-domain cross talk upon NO binding
Publication date: Available online 24 April 2019Source: Journal of Molecular Graphics and ModellingAuthor(s): Rana Rehan Khalid, Arooma Maryam, Vasiliki E. Fadouloglou, Abdul Rauf Siddiqi, Yang ZhangAbstractThe human soluble Guanylate Cyclase (hsGC) is a heterodimeric heme-containing enzyme which regulates many important physiological processes. In eukaryotes, hsGC is the only known receptor for nitric oxide (NO) signaling. Improper NO signaling results in various disease conditions such as neurodegeneration, hypertension, stroke and erectile dysfunction. To understand the mechanisms of these diseases, structure determinat...
Source: Journal of Molecular Graphics and Modelling - April 25, 2019 Category: Molecular Biology Source Type: research

Explaining the interactions between metaldehyde and acidic surface groups of activated carbon under different pH conditions
Publication date: Available online 21 April 2019Source: Journal of Molecular Graphics and ModellingAuthor(s): Anthuan Ferino-Pérez, Juan José Gamboa-Carballo, Zhuojun Li, Luiza C. Campos, Ulises Jáuregui-HazaAbstractMetaldehyde (MA) is an organic compound widely used in agriculture all around the world as molluscicide. There are growing concerns that relatively high levels of MA have been detected in surface water, which could be ascribed to the fact that it is transparent to common wastewater treatment processes. A theoretical study of the influence of activated carbon (AC) surface groups (SGs) on MA ...
Source: Journal of Molecular Graphics and Modelling - April 22, 2019 Category: Molecular Biology Source Type: research

HQSAR and random forest-based QSAR models for anti-T. vaginalis activities of nitroimidazoles derivatives
Publication date: Available online 19 April 2019Source: Journal of Molecular Graphics and ModellingAuthor(s): Gabriel Corrêa Veríssimo, Evaldo Francisco Menezes Dutra, Anna Letícia Teotonio Dias, Philipe de Oliveira Fernandes, Thales Kronenberger, Maria Aparecida Gomes, Vinicius Gonçalves MaltarolloAbstractTrichomonas vaginalis is the causative agent of trichomoniasis, a highly prevalent sexually transmitted infection worldwide. Nitroimidazole drugs, such as metronidazole and tinidazole, are the only recommended treatment, but cases of resistance represent at least 5%. In case of resistance or th...
Source: Journal of Molecular Graphics and Modelling - April 19, 2019 Category: Molecular Biology Source Type: research

Electronic structure and optical properties of the dialkali metal monotelluride compounds: Ab initio study
Publication date: Available online 19 April 2019Source: Journal of Molecular Graphics and ModellingAuthor(s): Z. Souadia, A. Bouhemadou, S. Bin-Omran, R. Khenata, Y. Al-Douri, S. Al EssaAbstractStructural parameters, electronic structure and optical properties of the dialkali metal monotelluride M2Te (M = Li, Na, K and Rb) compounds in the cubic antifluorite structure were investigated via ab initio calculations using the all electron linearized augmented plane wave approach based on density functional theory with and without including spin-orbit coupling (SOC). The exchange-correlation interactions were described with...
Source: Journal of Molecular Graphics and Modelling - April 19, 2019 Category: Molecular Biology Source Type: research

High pressure behavior of crystal [2,2′-bi(1,3,4-oxadiazole)]- 5,5′-dinitramide: A DFT investigation
Publication date: Available online 17 April 2019Source: Journal of Molecular Graphics and ModellingAuthor(s): Guozheng Zhao, Dongfang Yang, Jinjian Liu, Jianfeng Jia, Haishun WuAbstractDensity functional theory (DFT) computation was carried out to investigate the crystal, molecular and electronic structures of high energy crystal [2,2′-bi(1,3,4-oxadiazole)]-5,5′-dinitramide (BODN) with the pressure 0–120 GPa. The relaxed crystal structure by the GGA/PBE-TS functional matches well with the experimental data at ambient pressure condition. With the intensifying of pressure, the lattice parameters, volumes,...
Source: Journal of Molecular Graphics and Modelling - April 17, 2019 Category: Molecular Biology Source Type: research

Atomistic molecular dynamics simulations of the LCST conformational transition in Poly(N-Vinylcaprolactam) in water
Publication date: Available online 12 April 2019Source: Journal of Molecular Graphics and ModellingAuthor(s): Oleksii S. Zhelavskyi, Alexander KyrychenkoAbstractThermoresponsive poly (N-vinylcaprolactam) (PVCL) has received growing interest due to a temperature-induced phase transition, which switches its solubility in aqueous solutions. However, the lower critical solution temperature (LCST) of PVCL is greatly influenced by the molecular weight, morphology and the environment. Therefore, despite of numerous experimental studies of the thermal response of PVCL, a driving force and a molecular origin of conformation transit...
Source: Journal of Molecular Graphics and Modelling - April 13, 2019 Category: Molecular Biology Source Type: research

Deciphering the three-domain architecture in schlafens and the structures and roles of human schlafen12 and serpinB12 in transcriptional regulation
Publication date: Available online 9 April 2019Source: Journal of Molecular Graphics and ModellingAuthor(s): Jiaxing Chen, Leslie A. KuhnAbstractSchlafen proteins are important in cell differentiation and defense against viruses, and yet this family of vertebrate proteins is just beginning to be understood at the molecular level. Here, the three-dimensional architecture and molecular interfaces of human schlafen12 (hSLFN12), which promotes intestinal stem cell differentiation, are analyzed by sequence conservation and structural modeling in light of the functions of its homologs and binding partners. Our analysis shows tha...
Source: Journal of Molecular Graphics and Modelling - April 10, 2019 Category: Molecular Biology Source Type: research

Editorial Board
Publication date: June 2019Source: Journal of Molecular Graphics and Modelling, Volume 89Author(s): (Source: Journal of Molecular Graphics and Modelling)
Source: Journal of Molecular Graphics and Modelling - April 10, 2019 Category: Molecular Biology Source Type: research

Theoretical studies on the electronic structures and optical properties of (Cu, C)-codoped rutile TiO2 from GGA+U calculations
Publication date: Available online 5 April 2019Source: Journal of Molecular Graphics and ModellingAuthor(s): Rui-Qin Li, Dong-Xiang Li, Dan-Tong Zhou, Xin-Mao Qin, Wan-Jun YanAbstractThe electronic structures, formation energy and optical properties of Cu-doped, C-doped, and (Cu, C)-codoped TiO2 were investigated by the projector augmented wave (PAW) method within GGA + U approximation. The results show that the lattice distortion of the Cu@i1&C@i2 system is the largest in all doping systems. The optical absorption edges of the C@i system and the Cu@i1&C@i2 system appear a blue-shift, which is attributed ...
Source: Journal of Molecular Graphics and Modelling - April 5, 2019 Category: Molecular Biology Source Type: research

Docking software performance in protein-glycosaminoglycan systems
We present a benchmarking study for protein-glycosaminoglycan systems with eight docking programs: Dock, rDock, ClusPro, PLANTS, HADDOCK, Hex, SwissDock and ATTRACT. We used a non-redundant representative dataset of 28 protein-glycosaminoglycan complexes with experimentally available structures, where a glycosaminoglycan ligand was longer than a trimer. Overall, the ligand binding poses could be correctly predicted in many cases by the tested docking programs, however the ranks of the docking poses are often poorly assigned. Our results suggest that Dock program performs best in terms of the pose placement, has the most su...
Source: Journal of Molecular Graphics and Modelling - April 2, 2019 Category: Molecular Biology Source Type: research

Orthogonal order parameters to model the reaction coordinate of an enzyme catalyzed reaction
Publication date: Available online 30 March 2019Source: Journal of Molecular Graphics and ModellingAuthor(s): Sanjib Paul, Tanmoy Kumar Paul, Srabani TaraphderAbstractThe choice of suitable collective variables in formulating an optimal reaction coordinate is a challenging task for activated transitions between a pair of stable states especially when dealing with biochemical changes such as enzyme catalyzed reactions. A detailed benchmarking study is carried out on the choice of collective variables that can distinguish between the stable states unambiguously. We specifically address the issue if these variables may be dir...
Source: Journal of Molecular Graphics and Modelling - March 30, 2019 Category: Molecular Biology Source Type: research

Insights into the structure-affinity relationships and solvation effects between OfHex1 and inhibitors using molecular dynamics simulations
In this study, we examined the free energy patterns and per residue decomposition of binding within the complexes of OfHex1 and a series of inhibitors, utilizing restricted molecular dynamics (MD) and water-mediated MM/GBSA calculations. The results indicated Glu328 could form a stronger polar interaction with OfHex1 inhibitors, while Trp448 and Trp490 had important non-polar contributions. Interestingly, the conformation of Trp448 was different in the open or closed state, when OfHex1 bound different inhibitors. Moreover, the water molecule that mediates the GlcNAc Ⅱ and Trp490 may be critical to stabilizing the hydroph...
Source: Journal of Molecular Graphics and Modelling - March 28, 2019 Category: Molecular Biology Source Type: research

An anticoagulant peptide from Porphyra yezoensis inhibits the activity of factor XIIa: In vitro and in silico analysis
In this study, the coagulation factor XIIa activity in the presence of VITPOR AI was determined. Molecular modelling was performed to investigate the interaction between peptide and FXIIa. The structure of the peptide was predicted using PEP-FOLD3 server and simulated by molecular dynamics (MD) using GROMACS package. Molecular docking was carried out using peptide-protein docking software, pepATTRACT and its stability was confirmed by MD simulations. The chromogenic substrate assay revealed that the peptide inhibited the amidolytic activity of FXIIa with IC50 of 70.24 μM. The docking result showed peptide interactions...
Source: Journal of Molecular Graphics and Modelling - March 27, 2019 Category: Molecular Biology Source Type: research

In Silico insights on enhancing thermostability and activity of a plant Fructosyltransferase from Pachysandra terminalis via introduction of disulfide bridges
We report here the five mutants, M31C-Q49C, L144C-S193C, P34C-W300C, S219C-L226C and V470C-S498C with enhanced thermostabilities and/or activities relative to the wild type. Interestingly, M31C-Q49C, which is located within the catalytic-carrying blade of the catalytic domain, has an activity enhancement at both temperatures. At 334 K, three mutations, L144C-S193C, P34C-W300C and V470C-S498C, achieved thermostability relative to the wild type. Intriguingly, both activity and stability enhancement exhibited only at 334 K can be achieved provided that the mutation is located either on the catalytic-carrying residue blade...
Source: Journal of Molecular Graphics and Modelling - March 25, 2019 Category: Molecular Biology Source Type: research

Fe@(Au/Ag)n (n=1,12,54) core-shell nanoparticles as effective drug delivery vehicles for anti-cancer drugs: The computational study
Publication date: Available online 21 March 2019Source: Journal of Molecular Graphics and ModellingAuthor(s): Pourseyed Aghaei Fatematossadat, Mahnaz Mohammadi, S. Ehsan RoozmehAbstractIn this paper, we study magnetic and structural properties of silver and gold-coated iron nanoparticle as novel drug delivery systems for the two commercially famous cancer treatment drugs, using the density functional theory (DFT) computations.Our calculations show that silver and gold-coated iron nanoparticle have magnetization and the magnetic moment of the Fe atom in the Fe@(Ag/Au)n core-shells saturated to a value of about 3 μB. Thus...
Source: Journal of Molecular Graphics and Modelling - March 22, 2019 Category: Molecular Biology Source Type: research

An anticoagulant peptide from Porphyra yezoensis inhibits the activity of factor XIIa: In vitro and in silico analysis
In this study, the coagulation factor XIIa activity in the presence of VITPOR AI was determined. Molecular modelling was performed to investigate the interaction between peptide and FXIIa. The structure of the peptide was predicted using PEP-FOLD3 server and simulated by molecular dynamics (MD) using GROMACS package. Molecular docking was carried out using peptide-protein docking software, pepATTRACT and its stability was confirmed by MD simulations. The chromogenic substrate assay revealed that the peptide inhibited the amidolytic activity of FXIIa with IC50 of 70.24 μM. The docking result showed peptide interactions...
Source: Journal of Molecular Graphics and Modelling - March 22, 2019 Category: Molecular Biology Source Type: research

Molecular dynamics investigation on the Asciminib resistance mechanism of I502L and V468F mutations in BCR-ABL
In this study, molecular dynamics simulations and molecular mechanics generalized Born surface area (MM-GB/SA) calculations were performed to investigate the molecular mechanism of Asciminib resistance induced by the two mutants. The obtained results indicate that the mutations have adversely influence on the binding of Asciminib to BCR-ABL, as the nonpolar contributions decline in the two mutants. In addition, I502L mutation causes α-helix I’ (αI′) to shift away from the helical bundle composed of αE, αF, and αH, making the distance between αI’ and Asciminib increased....
Source: Journal of Molecular Graphics and Modelling - March 22, 2019 Category: Molecular Biology Source Type: research

Modeling of atomic-molecular structures by contiguous filling of space with Frank-Kasper atomic domains
Publication date: Available online 18 March 2019Source: Journal of Molecular Graphics and ModellingAuthor(s): Oleh H. Havrysh, Vladyslav Kholodovych, Evgen A. AndreevAbstractAn application of contiguous filling of space with convex polyhedra, also known as Frank-Kasper (FK) atomic domains is demonstrated here for modeling of atomic molecular structures.Both regular, when all polyhedron edges have equal length, and strained, depending on the topology of the polyhedron the length of its edges may slightly fluctuate from the common length, polyhedra are used. Polyhedra are connected to each other in agreement with Plateau's l...
Source: Journal of Molecular Graphics and Modelling - March 19, 2019 Category: Molecular Biology Source Type: research

Editorial Board
Publication date: May 2019Source: Journal of Molecular Graphics and Modelling, Volume 88Author(s): (Source: Journal of Molecular Graphics and Modelling)
Source: Journal of Molecular Graphics and Modelling - March 19, 2019 Category: Molecular Biology Source Type: research

In silico profiling the interaction mechanism of 2,5-diketopiperazine derivatives as oxytocin antagonists
Publication date: Available online 16 March 2019Source: Journal of Molecular Graphics and ModellingAuthor(s): Ming Yang, Jianghe Luo, Zhumei Zeng, Ling Yang, Limian Xu, Yan LiAbstractOxytocin plays a vital role in the occurrence of preterm birth by interacting with oxytocin receptor (OTR), and thus OTR antagonists provide effective approaches for the treatment of early birth. Presently, for purpose of exploring the structural traits affecting the antagonism potency, the up-to-date largest set of 121 2,5-diketopiperazine derivatives as OTR antagonists was subjected to ligand-based three-dimensional quantitative structure&nd...
Source: Journal of Molecular Graphics and Modelling - March 18, 2019 Category: Molecular Biology Source Type: research

New factor Xa inhibitors based on 1,2,3,4-tetrahydroquinoline developed by molecular modelling
Publication date: Available online 16 March 2019Source: Journal of Molecular Graphics and ModellingAuthor(s): Ivan Ilin, Elena Lipets, Alexey Sulimov, Danil Kutov, Khidmet Shikhaliev, Andrey Potapov, Michael Krysin, Fedor Zubkov, Lyudmila Sapronova, Fazoyl Ataullakhanov, Vladimir SulimovAbstractFactor Xa is a serine protease representing a crucial element in the coagulation process and an attractive target for anticoagulant therapy. At the present time there are several chemical classes of factor Xa inhibitors with proven activity. Furthermore, three factor Xa inhibitors have been approved for the medical use to date. Howe...
Source: Journal of Molecular Graphics and Modelling - March 18, 2019 Category: Molecular Biology Source Type: research

In-silico designing and characterization of binding modes of two novel inhibitors for CB1 receptor against obesity by classical 3D-QSAR approach
Publication date: Available online 17 March 2019Source: Journal of Molecular Graphics and ModellingAuthor(s): Naveed Khan, Sobia Ahsan Halim, Waqasuddin Khan, Syed Kashif Zafar, Zaheer Ul-HaqAbstractObesity is the fifth primary hazard for mortality in the world; hence different therapeutic targets are explored to overcome this problem. Endocannabinoid is identified as the emerging target for the treatment of obesity as Cannabinoid 1 (CB1) receptor over-activation resulted in abdominal obesity. Potent antagonists or inverse agonists for CB1 receptor are the new strategies to develop anti-obesity drugs. Here, ligand-based 3D...
Source: Journal of Molecular Graphics and Modelling - March 18, 2019 Category: Molecular Biology Source Type: research

OpenMX viewer: A web-based crystalline and molecular graphical user interface program
Publication date: Available online 15 March 2019Source: Journal of Molecular Graphics and ModellingAuthor(s): Yung-Ting Lee, Taisuke OzakiAbstractThe OpenMX Viewer (Open source package for Material eXplorer Viewer) is a web-based graphical user interface (GUI) program for visualization and analysis of crystalline and molecular structures and 3D grid data in the Gaussian cube format such as electron density and molecular orbitals. The web-based GUI program enables us to quickly visualize crystalline and molecular structures by dragging and dropping XYZ, CIF, or OpenMX input/output files, and analyze static/dynamic structura...
Source: Journal of Molecular Graphics and Modelling - March 16, 2019 Category: Molecular Biology Source Type: research

Molecular dynamics of carbon nanohorns and their complexes with cisplatin in aqueous solution
Publication date: Available online 15 March 2019Source: Journal of Molecular Graphics and ModellingAuthor(s): Eduardo R. Almeida, Leonardo A. De Souza, Wagner B. De Almeida, Hélio F. Dos SantosAbstractThe medication with Pt-based antitumor drug cisplatin has demonstrated effective results against cancer cells, despite the severe side effects due to the high toxicity associated with the low selectivity of these anticancer agents. An alternative to overcome or decrease the side effects is to use drug delivery systems, which can carry high doses of the anticancer drug and promote its slow and targeted release to the tu...
Source: Journal of Molecular Graphics and Modelling - March 15, 2019 Category: Molecular Biology Source Type: research

Development of a virtual reality platform for effective communication of structural data in drug discovery
Publication date: Available online 12 March 2019Source: Journal of Molecular Graphics and ModellingAuthor(s): Laura J. Kingsley, Vincent Brunet, Gerald Lelais, Steve McCloskey, Kelly Milliken, Edgardo Leija, Stephen R. Fuhs, Kai Wang, Edward Zhou, Glen SpraggonAbstractIn drug discovery, structural knowledge of a target enables structure-based design approaches and thereby reduces the time and labor required to develop a therapy. Whilst molecular graphics frameworks coupled with computational analysis are now ubiquitous tools for the structural and computational biologist, sharing the detailed visualization and derived stru...
Source: Journal of Molecular Graphics and Modelling - March 13, 2019 Category: Molecular Biology Source Type: research

Rational design of (D-A) copolymers towards high efficiency organic solar cells: DFT and TD-DFT study
Publication date: Available online 12 March 2019Source: Journal of Molecular Graphics and ModellingAuthor(s): Walid Taouali, Mark E. Casida, Sami Znaidia, Kamel AlimiAbstractIn this work, we focus on designing a donor copolymer for the improvement of photovoltaic performance. Using density functional theory and time-dependent density functional theory, we investigated the electronic, optical and charge transfer properties of a series of new designed copolymers based on the reported copolymer Pa0 which is composed of a donor fluorene unit and an acceptor 4,7-dithien-2-yl-2,1,3-benzothiadiazole. We first obtained two copolym...
Source: Journal of Molecular Graphics and Modelling - March 13, 2019 Category: Molecular Biology Source Type: research

Low susceptibility of asunaprevir towards R155K and D168A point mutations in HCV NS3/4A protease: A molecular dynamics simulation
Publication date: Available online 11 March 2019Source: Journal of Molecular Graphics and ModellingAuthor(s): Jirayu Kammarabutr, Panupong Mahalapbutr, Bodee Nutho, Nawee Kungwan, Thanyada RungrotmongkolAbstractHepatitis C has become an important health problem that requires expensive treatment and leads to liver tumorigenesis. Hepatitis C virus (HCV), which is the main cause of hepatitis C, has a high mutation rate due to the lack of proofreading activity of the RNA polymerase enzyme. The NS3/4A serine protease is an important target for anti-HCV drug discovery and development because of its crucial role in the cleavage o...
Source: Journal of Molecular Graphics and Modelling - March 12, 2019 Category: Molecular Biology Source Type: research

Impact sensitivity of aryl diazonium chlorides: Limitations of molecular and solid-state approach
Publication date: Available online 11 March 2019Source: Journal of Molecular Graphics and ModellingAuthor(s): Sergey V. BondarchukAbstractThe mechanism of the compression-induced decomposition of aryl diazonium chlorides is proposed on the basis of quantum-chemical calculations of both the isolated cations and crystalline materials. The electron transfer from the anion to the cation, followed by the crystal decomposition, is observed with the rise of pressure. Taking the known nature of the structural changes in cations undergone upon reduction, five structural, vibrational and electronic determinants of impact sensitivity...
Source: Journal of Molecular Graphics and Modelling - March 12, 2019 Category: Molecular Biology Source Type: research

Structure-based virtual screening for novel chymase inhibitors by in silico fragment mapping
Publication date: Available online 12 March 2019Source: Journal of Molecular Graphics and ModellingAuthor(s): Shin-ichiro Ozawa, Miki Takahashi, Noriyuki Yamaotsu, Shuichi HironoAbstractThe term chymase refers to a family of chymotrypsin-like serine proteases stored within the secretory granules of mast cells. Recently, a variety of small molecule inhibitors for chymase have been developed with a primary focus on the treatment of cardiovascular diseases. Despite the expected therapeutic benefit of these chymase inhibitors, they have not been used clinically. Here, we attempted to identify new chymase inhibitors using a mul...
Source: Journal of Molecular Graphics and Modelling - March 12, 2019 Category: Molecular Biology Source Type: research

Understanding structures and properties of phosphorene/perovskite heterojunction toward perovskite solar cell applications
This study helps the fundamental understanding of the interaction between the phosphorene and the halide perovskite materials, and could provide a foundation for the better understanding of the low-dimensional materials in perovskite-based optoelectronic devices.Graphical abstract (Source: Journal of Molecular Graphics and Modelling)
Source: Journal of Molecular Graphics and Modelling - March 12, 2019 Category: Molecular Biology Source Type: research

Understanding of the molecular mechanism of the phenylsulfenic acid elimination from nitroalkyl systems
Publication date: Available online 10 March 2019Source: Journal of Molecular Graphics and ModellingAuthor(s): Radomir JasińskiAbstractThe molecular mechanism of the phenylsulfenic acid elimination from nitroalkyl systems has been explored using M06-2X/6-31++G(d,p) theoretical level. It was found that independently of environment polarity as well as degree of screening of nitroalkyl moiety, these types of reactions proceed via one-step, polar mechanism with asynchronous transition state. According to actual state of knowledge this type of the mechanism should not be treated as “pericyclic”. Simultaneously, all ...
Source: Journal of Molecular Graphics and Modelling - March 11, 2019 Category: Molecular Biology Source Type: research

Refinement of the gonadotropin releasing hormone receptor I homology model by applying molecular dynamics
Publication date: Available online 11 March 2019Source: Journal of Molecular Graphics and ModellingAuthor(s): Haralambos Tzoupis, Agathi Nteli, Jamie Platts, Efi Mantzourani, Theodore TseliosAbstractSexual maturation of human cells in ovaries and prostate is linked to the biochemical cascade initiated by the activation of cell receptors through the binding of Gonadotropin Releasing Hormone (GnRH). The GnRH receptors (GnRHR) are part of the rhodopsin G-protein-coupled receptor (GPCR) family and consist of seven trans–membrane helical domains connected via extra– and intra–cellular segments. The GnRH–...
Source: Journal of Molecular Graphics and Modelling - March 11, 2019 Category: Molecular Biology Source Type: research

Second-order NLO properties of bis-cyclometalated iridium(Ⅲ) complexes: Substituent effect and redox switch
Publication date: Available online 9 March 2019Source: Journal of Molecular Graphics and ModellingAuthor(s): Xiang Li, Hong-Qiang Wang, Jin-Ting Ye, Yuan Zhang, Yong-Qing QiuAbstractThe iridium(III) complexes could be excellent second-order nonlinear optical (NLO) switch materials due to various advantages including abundant valence states, the diversity of coordination forms and rich electrochemical properties. In this work, the substituent effect and the multi-state switchable response of a series of novel Ir(CˆN)2ADC complexes (CˆN = cyclometalated ligands and ADC = diaminocarbene), induced by electroc...
Source: Journal of Molecular Graphics and Modelling - March 10, 2019 Category: Molecular Biology Source Type: research

On the mechanical stability and buckling analysis of carbon nanotubes filled with ice nanotubes in the aqueous environment: A molecular dynamics simulation approach
Publication date: Available online 6 March 2019Source: Journal of Molecular Graphics and ModellingAuthor(s): S. Ajori, A. Ameri, R. AnsariAbstractIn this article, molecular dynamics (MD) simulations are utilized to investigate the buckling behavior of carbon nanotubes (CNTs) containing ice nanotubes in the vacuum and aqueous environment. The obtained results show that unlike the critical strain, the critical buckling load of CNT containing ice nanotube is higher than that of pure CNT in the vacuum. It is also indicated that the sensitivity of critical buckling load and the critical strain of CNT containing ice nanotube to ...
Source: Journal of Molecular Graphics and Modelling - March 7, 2019 Category: Molecular Biology Source Type: research

Polyurethanases: Three-dimensional structures and molecular dynamics simulations of enzymes that degrade polyurethane
Publication date: Available online 6 March 2019Source: Journal of Molecular Graphics and ModellingAuthor(s): Vanessa Petry do Canto, Claudia Elizabeth Thompson, Paulo Augusto NetzAbstractThe global production of plastics increases every year, because these materials are widely used in several segments of modern life. Polyurethanes are a very important class of polymers, used in many areas of everyday life, from automotive equipments to mattresses. The waste management usually involves accumulation in landfills, incineration, and reuse processes. However, bioremediation processes are being increasingly tested, due to the ef...
Source: Journal of Molecular Graphics and Modelling - March 7, 2019 Category: Molecular Biology Source Type: research

Discovery of small molecule binders of human FSHR(TMD) with novel structural scaffolds by integrating structural bioinformatics and machine learning algorithms
ConclusionThe study proposes 1,3-diphenyl-1H-pyrazole-5-carboxylate as a promising scaffold for the design of new and potent FSHR allosteric inhibitors.Graphical abstract (Source: Journal of Molecular Graphics and Modelling)
Source: Journal of Molecular Graphics and Modelling - March 6, 2019 Category: Molecular Biology Source Type: research

Pharmacophore modeling and virtual screening studies to identify novel selective SIRT2 inhibitors
This study will hopefully provide a basis for developing potent and selective SIRT2 inhibitors.Graphical abstract (Source: Journal of Molecular Graphics and Modelling)
Source: Journal of Molecular Graphics and Modelling - March 6, 2019 Category: Molecular Biology Source Type: research

Hexagonal boron nitride nanosheet as novel drug delivery system for anticancer drugs: Insights from DFT calculations and molecular dynamics simulations
Publication date: Available online 2 March 2019Source: Journal of Molecular Graphics and ModellingAuthor(s): Morteza Vatanparast, Zahra ShariatiniaAbstractDensity functional theory (DFT) calculations and molecular dynamic (MD) simulations were accomplished to comprehend the nature of the interactions between 5-fluorouracil (FU)/6-mercaptopurine (MP)/6-thioguanine (TG) anticancer drugs and hexagonal boron nitride (BN) nanosheet as a drug delivery system. It is found from the calculations that the adsorption process of drug molecules on the BN nanosheet is exothermic and occurs spontaneously. The polarity for the drug loaded...
Source: Journal of Molecular Graphics and Modelling - March 5, 2019 Category: Molecular Biology Source Type: research

A DFT study on NO reduction to N2O using Al- and P-doped hexagonal boron nitride nanosheets
Publication date: Available online 4 March 2019Source: Journal of Molecular Graphics and ModellingAuthor(s): Mehdi D. Esrafili, Soheila Asadollahi, Safa HeydariAbstractUsing the dispersion-corrected DFT calculations, the catalytic reduction of NO molecules to N2O is investigated over Al- and P-doped hexagonal boron nitride nanosheets (h-BNNS). It is found that NO dissociation over both these surfaces needs a very large energy barrier, which indicates it cannot proceed at normal temperature. In contrast, the results show that NO molecules can be easily reduced into N2O via a dimer mechanism. The obtained activation energies...
Source: Journal of Molecular Graphics and Modelling - March 5, 2019 Category: Molecular Biology Source Type: research

The electronic, half-metallic, and magnetic properties of Ca1-xCrxS ternary alloys: Insights from the first-principle calculations
Publication date: Available online 26 February 2019Source: Journal of Molecular Graphics and ModellingAuthor(s): Mohammed M. Obeid, Hamad Rahman Jappor, Shaker J. Edrees, Majid M. Shukur, Rabah Khenata, Y. MogulkocAbstractThe electronic, structural, and magnetic characteristics of Cr atom substituting Ca atom in rocksalt CaS have been investigated within the formalism of (GGA + PBE) and PBE with Hubbard correction (GGA + U). Our findings point out that the ternary alloys are dynamically stable depending on the obtained results of elastic constants. For structural properties, it is clear that the lattice...
Source: Journal of Molecular Graphics and Modelling - February 27, 2019 Category: Molecular Biology Source Type: research

Structural significance of residues 158–160 in the H3N2 hemagglutnin globular head: A computational study with implications in viral evolution and infection
Publication date: Available online 25 February 2019Source: Journal of Molecular Graphics and ModellingAuthor(s): Marni E. Cueno, Hayato Shiotsu, Karin Nakano, Emiko Sugiyama, Mari Kikuta, Rikuya Usui, Riku Oya, Kenichi ImaiAbstractInfluenza A H3N2 has been linked to annual outbreaks within the human population attributable to continuous structural changes. H3N2 HA contains well identified antigenic sites and receptor-binding sites (RBS) that are possibly correlated to viral evolution and infection. However, the structural significance of amino acid residues associated with both viral evolution and infection were not fully ...
Source: Journal of Molecular Graphics and Modelling - February 26, 2019 Category: Molecular Biology Source Type: research

Conformational perturbation of peptides in presence of polar organic solvents
Publication date: Available online 25 February 2019Source: Journal of Molecular Graphics and ModellingAuthor(s): Neetu Singh Yadav, Devapriya ChoudhuryAbstractThe critical role played by solvent environment in maintaining the conformational integrity of peptides and proteins is accepted without question. Numerous experiments have suggested that perturbing the solvent environment of peptides and proteins by the addition of polar organic solvents have important consequences for the conformation of these molecules. However, experimental studies of such perturbations often report different kinds of effects depending on the sol...
Source: Journal of Molecular Graphics and Modelling - February 25, 2019 Category: Molecular Biology Source Type: research

Specific interactions between 2-trans enoyl-acyl carrier protein reductase and its ligand: Protein-ligand docking and ab initio fragment molecular orbital calculations
Publication date: Available online 25 February 2019Source: Journal of Molecular Graphics and ModellingAuthor(s): Naruedon Phusi, Riku Sato, Takuya Ezawa, Shogo Tomioka, Chayanin Hanwarinroj, Bandit Khamsri, Pharit Kamsri, Auradee Punkvang, Pornpan Pungpo, Noriyuki KuritaAbstract2-trans enoyl-acyl carrier protein reductase (InhA) has been identified as a promising target for the development of novel chemotherapy for tuberculosis. In the present study, a series of heteroaryl benzamide derivatives were selected as potent inhibitors against InhA, and their binding properties with InhA were investigated at atomic and electronic...
Source: Journal of Molecular Graphics and Modelling - February 25, 2019 Category: Molecular Biology Source Type: research

Exploring adsorption mechanism of hydrogen cyanide and cyanogen chloride molecules on arsenene nanoribbon from first-principles
Publication date: Available online 23 February 2019Source: Journal of Molecular Graphics and ModellingAuthor(s): R. Bhuvaneswari, V. Nagarajan, R. ChandiramouliAbstractThe SIESTA package is employed in examining the electronic and adsorption features of the toxic asphyxiants hydrogen cyanide (HCN) and cyanogen chloride (NCCl) on armchair arsenene (As-arm) nanoribbon. Based on the generalized gradient approximation (GGA) with the Perdew-Burke-Ernzerhof (PBE) level of theory, we explored the adsorption of HCN and NCCl on As-arm nanoribbon. The significant parameters necessary to validate the electronic and stable nature of A...
Source: Journal of Molecular Graphics and Modelling - February 24, 2019 Category: Molecular Biology Source Type: research

OxH2x+1+ clusters: A new series of non-metallic superalkali cations by trapping H3O+ into water
We report a new series of non-metallic superalkali cations, OxH2x+1+ (x = 1–5) using ab initio MP2/6–311++G(d,p) level. These cations are designed by successive hydration of the hydronium cation (OH3+), which can be expressed in the form of OH3+ … (x-1)H2O complexes. These OxH2x+1+ clusters possess a number of electrostatic as well as partially covalent H-bonds, with the interacting energy in the range 5.2–29.3 kcal/mol as revealed by quantum theory of atoms in molecules analyses. These cations are found to be stable against deprotonation as well as dehydration pathways, and their stability i...
Source: Journal of Molecular Graphics and Modelling - February 24, 2019 Category: Molecular Biology Source Type: research

α-methylation and α-fluorination electronic effects on the regioselectivity of carbonyl groups of uracil by H and triel bonds in the interaction of U, T and 5FU with HCl and TrH3 (Tr = B, Al)
Publication date: May 2019Source: Journal of Molecular Graphics and Modelling, Volume 88Author(s): Aristote Matondo, Renjith Thomas, Philippe Vuka Tsalu, Christian Tshikala Mukeba, Virima MudogoAbstractQuantum chemical calculations at the ωB97XD/6–311++G(d,p) level of theory have been executed to investigate the effect of substituents via hydrogen-bonded and triel-bonded complexes between uracil (U), thymine (T) and 5-fluorouracil (5FU) with HCl for the former complexes, and with BH3 and AlH3 for the latter complexes. These calculations are supported by single-point energy calculations at MP2/6–311++G(d,p...
Source: Journal of Molecular Graphics and Modelling - February 15, 2019 Category: Molecular Biology Source Type: research

Study of alpha-amylase and gold nanoparticles interaction at two different temperatures through molecular dynamics
Publication date: Available online 11 February 2019Source: Journal of Molecular Graphics and ModellingAuthor(s): S. Hooman Vahidi, Mohammad Reza Bozorgmehr, Ali Morsali, S. Ali BeyramabadiAbstractThe interaction of alpha-amylase with gold nanoparticles was studied at the two different temperatures of 25 and 75 °C through molecular dynamics simulation. To this end, 3-nm diameter spherical gold nanoparticles were designed. According to root mean square deviation results, at a high temperature, enzyme stability decreased in the absence of nanoparticles and increased in the presence of nanoparticles. Root mean square flu...
Source: Journal of Molecular Graphics and Modelling - February 12, 2019 Category: Molecular Biology Source Type: research

α-methylation and α-fluorination electronic effect on the regioselectivity of carbonyl groups of uracil by H and triel bonds in the interaction of U, T and 5FU with HCl and TrH3 (Tr = B, Al)
Publication date: Available online 10 February 2019Source: Journal of Molecular Graphics and ModellingAuthor(s): Aristote Matondo, Renjith Thomas, Philippe Vuka Tsalu, Christian Tshikala Mukeba, Virima MudogoAbstractQuantum chemical calculations at the ωB97XD/6–311++G(d,p) level of theory have been executed to investigate the effect of substituents via hydrogen-bonded and triel-bonded complexes between uracil (U), thymine (T) and 5-fluorouracil (5FU) with HCl for the former complexes, and with BH3 and AlH3 for the latter complexes. These calculations are supported by single-point energy calculations at MP2/6&nd...
Source: Journal of Molecular Graphics and Modelling - February 10, 2019 Category: Molecular Biology Source Type: research

Quantifying correlations between mutational sites in the catalytic subunit of γ-secretase
Publication date: Available online 8 February 2019Source: Journal of Molecular Graphics and ModellingAuthor(s): Cecilia Chávez-García, Rodrigo Aguayo-Ortiz, Laura DominguezAbstractPresenilin 1 (PS1) is the catalytic subunit of the γ-secretase complex which is involved in the generation of amyloid-β peptides (Aβ). Single point mutations in PS1 alter the cleavage pattern of the amyloid precursor protein (APP) and lead to the formation of aberrant Aβ peptides. To date, more than two hundred mutations distributed among almost a third of PS1's amino acids have been associated to the developmen...
Source: Journal of Molecular Graphics and Modelling - February 9, 2019 Category: Molecular Biology Source Type: research

Modeling MesoBioNano systems with MBN studio made easy
Publication date: Available online 7 February 2019Source: Journal of Molecular Graphics and ModellingAuthor(s): Gennady B. Sushko, Ilia A. Solov'yov, Andrey V. Solov'yovAbstractThis paper introduces MesoBioNano (MBN) Studio – a graphical user interface for a popular multiscale simulation package MBN Explorer. MBN Studio has been developed to facilitate setting up and starting MBN Explorer calculations, monitoring their progress and examining the calculation results. It is tailored for any calculations that are supported by MBN Explorer, such as for example the single-point energy calculations, structure optimization,...
Source: Journal of Molecular Graphics and Modelling - February 7, 2019 Category: Molecular Biology Source Type: research