Interaction studies of kidney biomarker volatiles on black phosphorene nanoring: A first-principles investigation
We report the electronic properties of black phosphorene nanoring (BPN) and adsorption behavior of chronic kidney disease biomarker vapors on BPN. The designed BPN is stable, which is ensured by the formation energy with a value of −3.857eV/atom. The band gap of BPN is recorded as 0.716eV showing the semiconductor property. The prominent kidney disease biomarker vapors, namely isoprene, pentanal, hexanal, heptanal are allowed to interact on BPN and studied based on adsorption property on BPN. Based on charge transfer, energy band gap variation and adsorption energy, we studied the adsorption behavior of BPN towards k...
Source: Journal of Molecular Graphics and Modelling - February 11, 2020 Category: Molecular Biology Source Type: research

An approach to generate DNA polyhedral links of one/two strands
Publication date: Available online 8 February 2020Source: Journal of Molecular Graphics and ModellingAuthor(s): Jinwei Duan, Lin Cui, Ying Wang, Huayu ZhengAbstractScientists can change programmed DNA strands to adjust edge length and vertex junction to control the 3D structures with precision space signatures. The number of strands plays an important role in sequence design, synthesis and constitutive property. However, the majority of DNA branched polyhedra comprise a number of single strands. Therefore, it is crucial to make the number of strands to be calculated as less as possible. DNA polyhedral links are regarded as...
Source: Journal of Molecular Graphics and Modelling - February 10, 2020 Category: Molecular Biology Source Type: research

A computational study on the BN-yne sheet application in the Na-ion batteries
Publication date: Available online 7 February 2020Source: Journal of Molecular Graphics and ModellingAuthor(s): Ali Moalla, Maziar Noei, Fereydoon Khazali, Afsaneh MalekiAbstractAlthough Li-ion batteries are extensively applied, short lifetime, high cost, and safety problems limit their application. Na-ion batteries (NIB) might be an alternative to the Li-ion owing to wide availability, low cost, and nontoxicity of Na. Here, we performed density functional theory calculations to investigate the possible application of a graphyne-like BN layer (BN-yne) in the anode of NIBs. The adsorption energies of Na and Na+ on the BN-yn...
Source: Journal of Molecular Graphics and Modelling - February 8, 2020 Category: Molecular Biology Source Type: research

Bioconformational modulation of a thymidine kinase enzyme ligand through F⋯HO intramolecular hydrogen bond
Publication date: Available online 6 February 2020Source: Journal of Molecular Graphics and ModellingAuthor(s): Francisco A. Martins, Matheus P. FreitasAbstractWhile the induced-fit of a ligand towards an enzyme is pivotally dictated by intermolecular hydrogen bonds between the small molecule and amino acid residues in the binding site, the role of intramolecular hydrogen bond as contributing interaction for a bioactive conformation is not well understood. This work reports a theoretical conformational analysis of a thymidine kinase enzyme ligand (NMF) that is prone to experience an F⋯HO intramolecular hydrogen bond, ins...
Source: Journal of Molecular Graphics and Modelling - February 8, 2020 Category: Molecular Biology Source Type: research

Effects of tosyl-l-arginine methyl ester (TAME) on the APC/c subunits: An in silico investigation for inhibiting cell cycle
In conclusion, IR binding pocket can serve as an appropriate potential target for TAME as an inhibitor of APC/c.Graphical abstract (Source: Journal of Molecular Graphics and Modelling)
Source: Journal of Molecular Graphics and Modelling - February 7, 2020 Category: Molecular Biology Source Type: research

Editorial Board
Publication date: May 2020Source: Journal of Molecular Graphics and Modelling, Volume 96Author(s): (Source: Journal of Molecular Graphics and Modelling)
Source: Journal of Molecular Graphics and Modelling - February 7, 2020 Category: Molecular Biology Source Type: research

Potential tripeptides against the tyrosine kinase domain of human epidermal growth factor receptor (HER) 2 through computational and kinase assay approaches
Publication date: Available online 4 February 2020Source: Journal of Molecular Graphics and ModellingAuthor(s): Supaphorn Seetaha, Bundit Boonyarit, Sissades Tongsima, Napat Songtawee, Kiattawee ChoowongkomonAbstractAn abnormal activation of human epidermal growth factor receptor (HER) 2 has been found to associate with several types of human cancer, and thus the protein is a prominent target for cancer therapy. Although several small chemical molecules targeting the tyrosine kinase (TK) of HER family have been identified, the development of a new class of inhibitors, i.e., small peptides inhibiting the function of tyrosin...
Source: Journal of Molecular Graphics and Modelling - February 4, 2020 Category: Molecular Biology Source Type: research

Identification of potential natural neuroprotective molecules for Parkinson’s disease by using chemoinformatics and molecular docking
In this study, we used chemoinformatics tools and molecular docking simulations to analyze molecules that have been experimentally tested and bound to α-synuclein, causing neuroprotective or neurotoxic activity, and whose results have been used to select potential natural neuroprotective molecules. We identified 6 potential natural neuroprotective molecules that are similar in their chemical structure to neuroprotective molecules and have a high number of hydrogen bonds with α-synuclein. We expect that these molecules may lead to the design or discovery of new effective treatments for Parkinson’s disease....
Source: Journal of Molecular Graphics and Modelling - February 4, 2020 Category: Molecular Biology Source Type: research

Effect of 3d heterometallic ions on the magnetic properties of azido-Cu(II) with isonicotinic acid coligands: A theoretical perspective
Publication date: Available online 3 February 2020Source: Journal of Molecular Graphics and ModellingAuthor(s): Shuchang Luo, Hong Mei, Xiaoyuan Sun, Pengfei ZhengAbstractBased on density functional theory and the broken-symmetry approach, the magnetic properties of an azido-Cu(II) complex with isonicotinic acid coligands were studied at the B1LYP/def2-TZVP level. According to the molecular magnetic orbitals and Mulliken spin population analysis, there are strong orbital interactions between the paramagnetic CuII/NiII ions and the bridging azide ligands and isonicotinic ions. The supposedly empty 4s/4p/4d orbitals of the M...
Source: Journal of Molecular Graphics and Modelling - February 4, 2020 Category: Molecular Biology Source Type: research

Aggregation behaviors of thermo-responsive methylcellulose in water: A molecular dynamics simulation study
Publication date: Available online 30 January 2020Source: Journal of Molecular Graphics and ModellingAuthor(s): Yang Yang, Wei Wu, Hongchen Liu, Hong Xu, Yi Zhong, Linping Zhang, Zhize Chen, Xiaofeng Sui, Zhiping MaoAbstractThe aggregation behaviors of methylcellulose (MC) in aqueous solution were investigated using all-atom molecular dynamic simulations (MD). The interactions between MC chains and water molecules at different temperatures were investigated by a series of MD analyses, such as the solvent accessible surface area, number of hydrogen bonds, radial distribution functions and the interaction energies. Constant ...
Source: Journal of Molecular Graphics and Modelling - February 1, 2020 Category: Molecular Biology Source Type: research

Understanding the potency of malarial ligand (D44) in plasmodium FKBP35 and modelled halogen atom (Br, Cl, F) functional groups
Publication date: Available online 31 January 2020Source: Journal of Molecular Graphics and ModellingAuthor(s): Palanisamy Deepa, Duraisamy ThirumeignanamAbstractThe present study clearly depicts the understanding of the D44 in Plasmodium FKBP35 around the hinge region. To analyse the binding stability of D44 ligand and to understand the role of halogen bond, hydrogen bond interaction formed between the hinge region amino acids: Isoleucine (Ile74), Phenylalanine (Phe54), Aspartic acid (Asp55) Phenylalanine (Phe64),Tyrosine (Tyr100), Tryptophan (TRP 77) and ligand D44 was portrayed specifically through interaction energy ca...
Source: Journal of Molecular Graphics and Modelling - February 1, 2020 Category: Molecular Biology Source Type: research

A theoretical study on the metal-free triazole formation through tandem [3+2] cycloaddition/retro-Diels-Alder reaction of benzyl azide and oxanorbornadienedicarboxylate
Publication date: Available online 28 January 2020Source: Journal of Molecular Graphics and ModellingAuthor(s): Mahshid Hamzehloueian, Rahman Hosseinzadeh, Setayesh GhandiyarAbstractA density functional theory study was performed on the mechanism and site selectivity of a domino [3 + 2] cycloaddition/retro-Diels-Alder reaction between benzyl azide and 7-oxabicyclo [2.2.1]hepta-2,5-diene-2,3-dicarboxylate (oxanorbornadienedicarboxylate) which provide a stable 1,2,3-triazole and the results were compared with the click reaction between benzyl azide and dimethyl acetylenedicarboxylate (DMAD) with similar triazole pr...
Source: Journal of Molecular Graphics and Modelling - January 29, 2020 Category: Molecular Biology Source Type: research

In silico mutagenesis in recombinant human keratinocyte growth factor: Improvement of stability and activity in addition to decrement immunogenicity
In conclusion, this study, for the first time, offered that the combine1 and F63Y mutants could highly improve the stability and activity of rhKGF and even reduce immunogenicity without having any significant effect on the biological functions of rhKGF.Graphical abstract (Source: Journal of Molecular Graphics and Modelling)
Source: Journal of Molecular Graphics and Modelling - January 29, 2020 Category: Molecular Biology Source Type: research

Theoretical investigation on radical anion promoted electrocyclization in photochromes
Publication date: Available online 27 January 2020Source: Journal of Molecular Graphics and ModellingAuthor(s): Nadia Bibi, Naveen Kosar, Khurshid Ayub, Tariq MahmoodAbstractRapid electrocyclization is proposed under radical anionic conditions in organic photochromes. DFT calculations have been performed to investigate the radical anion mediated electrocyclization in different organic photochromes. Furthermore, the activation barriers under radical anionic conditions are compared with those in neutral and radical cationic conditions. The nuclear independent chemical shift (NICS(0)) and synchronicity calculations have been ...
Source: Journal of Molecular Graphics and Modelling - January 29, 2020 Category: Molecular Biology Source Type: research

Push-pull nitronates in the [3+2] cycloaddition with nitroethylene: Molecular Electron Density Theory study
Publication date: Available online 28 January 2020Source: Journal of Molecular Graphics and ModellingAuthor(s): Agnieszka Kącka-ZychAbstractThe structure and the participation of the N-methoxy-N-[bis(methoxycarbonyl)methylene]amine N-oxide as model push-pull nitronate 1 with nitroethylene 2 in [3 + 2] cycloaddition (32CA) reaction have been analyzed within the Molecular Electron Density Theory (MEDT) using Density Functional Theory (DFT) calculations at the B3LYP(PCM)/6-31G(d) level. Topological analysis of the Electron Localization Function (ELF) of nitronate 1 reveals that this compound has pseudoradical cente...
Source: Journal of Molecular Graphics and Modelling - January 29, 2020 Category: Molecular Biology Source Type: research

Mg2+ vs Ca2+ bound active site of group II intron– A MD study
Publication date: Available online 23 January 2020Source: Journal of Molecular Graphics and ModellingAuthor(s): Abhishek Kumar, Priyadarshi SatpatiAbstractGroup II introns are enzymes which undergo self-splicing and remove itself from pre-messenger RNA. X-ray structures of group II intron of Oceanobacillus iheyensis at various stages of the self-splicing pathway (pre-hydrolytic, post-hydrolytic, and ligand-free state) revealed intricate atomic interaction network in the active site of the intron. It has been confirmed that a heteronuclear metal ion cluster consisting of four metal ions (K1, K2 sites with K+ and M1, M2 site...
Source: Journal of Molecular Graphics and Modelling - January 24, 2020 Category: Molecular Biology Source Type: research

Identification of potential natural neuroprotective molecules for Parkinson's disease by using chemoinformatics and molecular docking
In this study, we used chemoinformatics tools and molecular docking simulations to analyze molecules that have been experimentally tested and bound to α-synuclein, causing neuroprotective or neurotoxic activity, and whose results have been used to select potential natural neuroprotective molecules. We identified 6 potential natural neuroprotective molecules that are similar in their chemical structure to neuroprotective molecules and have a high number of hydrogen bonds with α-synuclein. We expect that these molecules may lead to the design or discovery of new effective treatments for Parkinson's disease.Graphi...
Source: Journal of Molecular Graphics and Modelling - January 24, 2020 Category: Molecular Biology Source Type: research

Characterisation of a catalytic triad and reaction selectivity in the dual mechanism of the catalyse hydride transfer in xylitol phosphate dehydrogenase
This study would assist future mutagenesis study and enzyme modification work to increase the catalysis efficiency of xylitol production in the industry.Graphical abstract (Source: Journal of Molecular Graphics and Modelling)
Source: Journal of Molecular Graphics and Modelling - January 24, 2020 Category: Molecular Biology Source Type: research

Theoretical study of electronic transport through P-porphyrin and S-porphyrin nanoribbons
Publication date: Available online 23 January 2020Source: Journal of Molecular Graphics and ModellingAuthor(s): Rajkumar Mondal, Barnali Bhattachrya, N. Bedamani Singh, Utpal SarkarAbstractElectronic transport through P-porphyrin and S-porphyrin nanoribbons have been studied by using nonequilibrium Green's function formalism (NEGF) combined with density functional theory (DFT) method. Band structure of both nanoribbons shows metallic behavior and bands near the Fermi level contain π character contributed by py orbital. Both nanoribbons exhibit metal-like conduction at extreme low bias. A remarkable negative differential...
Source: Journal of Molecular Graphics and Modelling - January 23, 2020 Category: Molecular Biology Source Type: research

Planarity does not always mean higher aromaticity – Intriguing metalloaromaticity of three Al13+ isomers
Publication date: Available online 23 January 2020Source: Journal of Molecular Graphics and ModellingAuthor(s): Surajit Guin, Sourav Ranjan Ghosh, Atish Dipankar JanaAbstractA pair of Al13+ clusters, one perfectly planar (CI) and another quasi-planar structure (CII) have been reported recently by our group [Guin et al. Journal of Molecular Modeling, 2018, 24, 344]. Both these clusters are rare examples of metal-aromatic systems having unique aromatic character. In these clusters localized strong anti-aromatic deltas are embedded within a strong aromatic sea. The quasi-planar CII structure is a true minimum structure with z...
Source: Journal of Molecular Graphics and Modelling - January 23, 2020 Category: Molecular Biology Source Type: research

Peri-, Chemo-, Regio-, Stereo- and Enantio-Selectivities of 1,3-dipolar cycloaddition reaction of C,N-Disubstituted nitrones with disubstituted 4-methylene-1,3-oxazol-5(4H)- one: A quantum mechanical study
Publication date: Available online 21 January 2020Source: Journal of Molecular Graphics and ModellingAuthor(s): George Baffour Pipim, Ernest Opoku, Richard Tia, Evans AdeiAbstractThe peri-, chemo-, regio-, stereo- and enantio-selectivities of 1,3-dipolar cycloaddition reaction of C,N-disubstituted nitrones with disubstituted 4-methylene-1,3-oxazol-5(4H)-one have been studied using density functional theory (DFT) at the M06–2X/6-311G (d,p) level of theory. The 1,3-dipole preferentially adds chemo-selectively across the olefinic bond in a (3 + 2) fashion forming the corresponding spirocycloadduct. The titled ...
Source: Journal of Molecular Graphics and Modelling - January 22, 2020 Category: Molecular Biology Source Type: research

Optimization of CHARMM force field parameters of a prostate cancer drug enzalutamide
Publication date: Available online 20 January 2020Source: Journal of Molecular Graphics and ModellingAuthor(s): Sefer BadayAbstractEnzalutamide is the most recent and potent clinically available drug molecule used to treat castration-resistant metastatic prostate cancer patients. In the presence of certain mutations on the Androgen receptor, enzalutamide fails to function as an antagonist. The molecular mechanism of this resistance has not been understood clearly. Molecular Dynamics (MD) simulations are a powerful tool to investigate such resistance mechanisms. Insights from MD simulations of receptor-ligand complex heavil...
Source: Journal of Molecular Graphics and Modelling - January 20, 2020 Category: Molecular Biology Source Type: research

Pair interaction energy decomposition analysis (PIEDA) and experimental approaches for investigating water interactions with hydrophilic and hydrophobic membranes
Publication date: Available online 18 January 2020Source: Journal of Molecular Graphics and ModellingAuthor(s): Mahboobeh Maghami, Amira AbdelrasoulAbstractThe origins of low and high interactions of polar groups with water molecules are still unknown and need to be further examined for effective future membrane synthesis and modification. The primary aim of this research study is to provide a comprehensive overview of the interactions at the molecular level occurring between water molecules and the fragments of hydrophobic and hydrophilic membranes based on pair interaction energy decomposition analysis (PIEDA) as part of...
Source: Journal of Molecular Graphics and Modelling - January 18, 2020 Category: Molecular Biology Source Type: research

Towards chemically accurate QM/MM simulations on GPUs
Publication date: Available online 16 January 2020Source: Journal of Molecular Graphics and ModellingAuthor(s): Ádám Jász, Ádám Rák, István Ladjánszki, Gábor János Tornai, György CsereyAbstractComputational chemistry simulations are extensively used to model natural phenomena. To maintain performance similar to molecular mechanics, but achieve comparable accuracy to quantum mechanical calculations, many researchers are using hybrid QM/MM methods. In this article we evaluate our GPU-accelerated ONIOM implementation by measurements on the crambin and ...
Source: Journal of Molecular Graphics and Modelling - January 17, 2020 Category: Molecular Biology Source Type: research

Reveal the interaction mechanism of five old drugs targeting VEGFR2 through computational simulations
Publication date: Available online 16 January 2020Source: Journal of Molecular Graphics and ModellingAuthor(s): Yonghui Lv, Yu Wang, Xin Zheng, Guizhao LiangAbstractVEGFR2, vascular endothelial growth factor receptor 2, plays an important role in anti-angiogenesis and is an effective target for inhibiting tumor cell proliferation and metastasis. Many small molecule inhibitors have so far exhibited fine therapeutic effects but do not rule out some adverse reactions. From the perspective of the new use of old drugs, we use a combination of two different docking methods, molecular dynamics simulations and quantum-chemical cal...
Source: Journal of Molecular Graphics and Modelling - January 17, 2020 Category: Molecular Biology Source Type: research

Borophene as an electronic sensor for metronidazole drug: A computational study
Publication date: Available online 13 January 2020Source: Journal of Molecular Graphics and ModellingAuthor(s): Chi Xiao, Kun Ma, Guofeng Cai, Xinyu Zhang, Esmail VessallyAbstractThe electronic sensitivity and reactivity of a B36 borophene are scrutinized toward the metronidazole (ML) drug using density functional theory calculations. The drug is mainly adsorbed via its –NO2 group on the edge of the B36 borophene. In the gas phase, the adsorption energy and Gibbs free energy change are about −22.1 and −19.3 kcal/mol, respectively. Because of a large HOMO destabilization upon the ML adsorption, the HOMO-...
Source: Journal of Molecular Graphics and Modelling - January 14, 2020 Category: Molecular Biology Source Type: research

Evaluation of consensus scoring methods for AutoDock Vina, smina and idock
Publication date: Available online 13 January 2020Source: Journal of Molecular Graphics and ModellingAuthor(s): Lily Masters, Scott Eagon, Michael HeyingAbstractWe investigated the application of consensus scoring using the freely available and open source structure-based virtual screening docking programs AutoDock Vina, smina and idock. These individual programs and several simple consensus scoring methods were tested for their ability to identify hits against 20 DUD-E benchmark targets using the AUC and EF1 metrics. We found that all of the consensus scoring methods, however normalized, fared worse, on average, than simp...
Source: Journal of Molecular Graphics and Modelling - January 13, 2020 Category: Molecular Biology Source Type: research

Predictive compression of molecular dynamics trajectories
Publication date: Available online 13 January 2020Source: Journal of Molecular Graphics and ModellingAuthor(s): Jan Dvořák, Martin Maňák, Libor VášaAbstractMolecular dynamics simulations help to understand the complex behavior of molecules. The output of such a simulation describes the trajectories of individual atoms as snapshots of atom positions in time. Many compression schemes were developed to reduce the amount of data needed for storing long trajectories. This is achieved by limiting the precision of coordinates, encoding differences instead of absolute values, dimensionality reduction ...
Source: Journal of Molecular Graphics and Modelling - January 13, 2020 Category: Molecular Biology Source Type: research

CuN3 doped graphene as an active electrocatalyst for oxygen reduction reaction in fuel cells: A DFT study
Publication date: Available online 11 January 2020Source: Journal of Molecular Graphics and ModellingAuthor(s): Nafiseh Mohammadi-rad, Mehdi D. Esrafili, Jaber Jahanbin SardroodiAbstractBased on first-principles DFT calculations, copper-nitrogen embedded graphene (CuN3-Gra) is introduced as an efficient electrocatalyst for oxygen reduction reaction (ORR) in fuel cells. The possible reaction mechanisms as well as the corresponding stationary points on potential energy surfaces are studied in acidic media. Our results indicate that dissociation of O2 over CuN3-Gra cannot occur at normal condition due to its large energy barr...
Source: Journal of Molecular Graphics and Modelling - January 12, 2020 Category: Molecular Biology Source Type: research

Elucidating the effect of static electric field on Amyloid Beta 1–42 supramolecular assembly
Publication date: Available online 12 January 2020Source: Journal of Molecular Graphics and ModellingAuthor(s): S. Muscat, F. Stojceski, A. DananiAbstractAmyloid-β (Aβ) aggregation is recognized to be a key toxic factor in the pathogenesis of Alzheimer disease, which is the most common progressive neurodegenerative disorder. In vitro experiments have elucidated that Aβ aggregation depends on several factors, such as pH, temperature and peptide concentration. Despite the research effort in this field, the fundamental mechanism responsible for the disease progression is still unclear. Recent research has propo...
Source: Journal of Molecular Graphics and Modelling - January 12, 2020 Category: Molecular Biology Source Type: research

The effect of calcium binding on the unfolding force of mutated and healthy titin I10 domain: A steered molecular dynamics simulation study
Publication date: Available online 10 January 2020Source: Journal of Molecular Graphics and ModellingAuthor(s): Mohadese Abidi, Reza SoheilifardAbstractTitin plays an important role in eccentric contraction by creating elastic property in the sarcomere. It can restore muscle to its rest length by stretching and increasing its length. Titin's structure is made of 244 domains. Due to its position, the I10 domain can be subjected to a mutation which leads to Arrhythmogenic cardiomyopathy. Furthermore, the calcium ion has an important role in muscle contractions by binding to some domains like I10 in titin and accordingly crea...
Source: Journal of Molecular Graphics and Modelling - January 11, 2020 Category: Molecular Biology Source Type: research

Experimental and numerical study of SO2 removal from a CO2/SO2 gas mixture in a Cu-BTC metal organic framework
Publication date: Available online 9 January 2020Source: Journal of Molecular Graphics and ModellingAuthor(s): H. Wang, J.Q. Bai, Y. Yin, S.F. WangAbstractThe mechanism of SO2 removal from a CO2/SO2 gas mixture in a copper benzene-1, 3, 5-tricarboxylate (Cu-BTC) material is investigated at the molecular level by the grand canonical Monte Carlo method. The effects of seven kinds of force-field relationships among CO2, SO2 and Cu-BTC on the selectivity for a SO2/CO2 gas mixture at different temperatures are studied in detail. The accuracy of the simulation model is validated by the experimental data. The results show that mo...
Source: Journal of Molecular Graphics and Modelling - January 10, 2020 Category: Molecular Biology Source Type: research

Elucidating the preference of dimeric over monomeric form for thermal stability of Thermus thermophilus isopropylmalate dehydrogenase: A molecular dynamics perspective
Publication date: Available online 10 January 2020Source: Journal of Molecular Graphics and ModellingAuthor(s): Reetu Sharma, Someswar Rao Sagurthi, G. Narahari SastryAbstractAn oligomer usually refers to a macromolecular complex formed by non-covalent interactions of monomers. Several thermophilic proteins are oligomers. The significance of oligomerization of individual proteins for stability at higher temperature is of prime importance for understanding evolution and increasing industrial productivity. The functional form of Thermus thermophilius isopropylmalate dehydrogenase (IPMDH), a widely studied protein to understa...
Source: Journal of Molecular Graphics and Modelling - January 10, 2020 Category: Molecular Biology Source Type: research

The effect of adsorption and grafting on the acidity of [(HSO3)C3C1im]+[Cl]− on the surface of (SiO2)4O2H4 clusters
Publication date: Available online 30 December 2019Source: Journal of Molecular Graphics and ModellingAuthor(s): Qiusheng Yang, Hansen Yang, Xiaoshu Ding, Wei Xue, Shujuan SunAbstractBoth adsorption and graft of active components on the surface of the silica are paramount methods for preparing heterogeneous catalysts. In this paper, the acidity of [(HSO3)C3C1im]+[Cl]− adsorbed and grafted on the surface of silica clusters was calculated at the level of B3LYP-d3/6-311++g(d, p). The results showed that both methods can enhance the acidity of the ionic liquids (ILs). The hydroxyl group on the carrier surface can increas...
Source: Journal of Molecular Graphics and Modelling - December 30, 2019 Category: Molecular Biology Source Type: research

Gas-phase electronic properties of tri-cationic imidazolium-based ionic liquids in comparison with mono- and di-cationic ionic liquids
Publication date: Available online 30 December 2019Source: Journal of Molecular Graphics and ModellingAuthor(s): Azim Soltanabadi, Maryam BahramiAbstractThe optimized geometries, electronic structures, and gas-phase properties of widely applicable non-linear trigeminal tri-cationic ILs (TT-X3) were investigated using density functional theory (DFT) calculations and compared with mono- (M-X) and di-cationic (D-X2) ionic liquids. The studied ILs are based on the imidazolium cation containing halide (X¯) anions, where X¯ = Cl¯, Br¯ and I¯. Inter-molecular hydrogen bonds were studied by atoms in mo...
Source: Journal of Molecular Graphics and Modelling - December 30, 2019 Category: Molecular Biology Source Type: research

Identification of potential platelet-derived growth factor receptor α inhibitors by computational screening and binding simulations
In this study, two types of pharmacophore model, which generated by ligand-based and receptor-based method, were put forward to identify novel chemical entities as PDGFRα inhibitors. It was found that some pharmacophore characteristics established by the two approaches overlap each other. In order to elucidate detailed interactions, representative molecules were selected to predict the conformations and binding modes of the molecules by molecular docking method. The calculation results of binding free energy illustrated that the van der Waals energy and nonpolar solvation were the most prominent contribution to the i...
Source: Journal of Molecular Graphics and Modelling - December 30, 2019 Category: Molecular Biology Source Type: research

Use of the index of ideality of correlation to improve aquatic solubility model
Publication date: Available online 28 December 2019Source: Journal of Molecular Graphics and ModellingAuthor(s): Andrey A. Toropov, Alla P. Toropova, Marco Marzo, Emilio BenfenatiAbstractModels for water solubility are built up using so-called correlation weights of fragments of simplified molecular input-line entry system (SMILES), 2D graph invariants, and hierarchy of rings present in molecules. The approach is based on Monte Carlo optimization of the molecular features. Two versions of the optimization were examined: (i) the traditional version; and (ii) the Index of Ideality of Correlation (IIC) version. The statistica...
Source: Journal of Molecular Graphics and Modelling - December 29, 2019 Category: Molecular Biology Source Type: research

Editorial Board
Publication date: March 2020Source: Journal of Molecular Graphics and Modelling, Volume 95Author(s): (Source: Journal of Molecular Graphics and Modelling)
Source: Journal of Molecular Graphics and Modelling - December 29, 2019 Category: Molecular Biology Source Type: research

Systematic molecular profiling of inhibitor response to the clinical missense mutations of ErbB family kinases in human gastric cancer
In this study, systematic inhibitor response to ErbB missense mutations in gastric cancer (GC) is investigated by combining computational analysis and experimental assay. The response profile is created for 6 ATP-competitive, reversible inhibitors against 9, 17, 5 and 17 GC-associated missense mutations of ErbB1, ErbB2, ErbB3 and ErbB4 kinase domains, respectively. From the profile a number of potential resistant and sensitive responses are identified theoretically. It is suggested that most ErbB mutations have only a modest effect on inhibitor binding, but few that are located around the kinase active site can influence...
Source: Journal of Molecular Graphics and Modelling - December 27, 2019 Category: Molecular Biology Source Type: research

Ultrasonic waves effect on S-shaped β-amyloids conformational dynamics by non-equilibrium molecular dynamics simulations
Publication date: Available online 24 December 2019Source: Journal of Molecular Graphics and ModellingAuthor(s): Marcello Miceli, Stefano Muscat, Umberto Morbiducci, Marco Cavaglià, Marco Agostino DeriuAbstractUltrasound-based technologies are widely adopted in the clinical practice. Recently, the ultrasound stable cavitation has been proposed as a strategy to destabilize amyloid aggregates in Alzheimer disease. However, the molecular mechanisms driving ultrasound-induced amyloid destabilization are not fully clarified yet. Here, molecular dynamics is applied to investigate in silico the conformational dynamics indu...
Source: Journal of Molecular Graphics and Modelling - December 26, 2019 Category: Molecular Biology Source Type: research

A molecular interaction field describing nonconventional intermolecular interactions and its application to protein–ligand interaction prediction
In this study, we developed a novel MIF calculation method that describes nonconventional interactions. This method evaluates the MIF as the interaction energy between the target ligand molecule and probe molecule. To describe the nonconventional interactions, our method employs quantum chemical calculations with four types of probe molecules. The calculated MIFs for casein kinase 2 (CK2) inhibitors correctly identify the halogen bond, CH/π, and CH/O interactions formed in the CK2/inhibitor complexes. Additionally, we have developed a method for calculating the protein–ligand interaction energy (Eint) based on the...
Source: Journal of Molecular Graphics and Modelling - December 24, 2019 Category: Molecular Biology Source Type: research

A first principles investigation on the influence of transition-metal elements on the structural, mechanical, and anisotropic properties of CaM2Al20 intermetallics
Publication date: Available online 23 December 2019Source: Journal of Molecular Graphics and ModellingAuthor(s): Xudong Zhang, Tianhui Dong, He Ma, Dongzhi Li, Caihong Ying, Cong Liu, Feng WangAbstractThe anisotropy in elasticity, mechanical properties and electronic properties of CaM2Al20 (M = V, Nb, Cr, Ti, Mo and Ta) compounds were investigated using the first-principle calculations. These ternary compounds are structurally stable according to the obtained phonon frequencies and formation enthalpy. The results of elastic modulus, hardness and elastic constants explain that CaM2Al20 intermetallics have higher hardnes...
Source: Journal of Molecular Graphics and Modelling - December 24, 2019 Category: Molecular Biology Source Type: research

A classification model for blood brain barrier penetration
In this study, we aimed to build improved BBB classification models using a large curated dataset of 605 compounds with two classification thresholds (threshold-1: Brain/Plasma ≥ 0.6 as BBB+ and Brain/Plasma0.6 as BBB+ and Brain/Plasma
Source: Journal of Molecular Graphics and Modelling - December 21, 2019 Category: Molecular Biology Source Type: research

A computational study on the role of water and conformational fluctuations in Hsp90 in response to inhibitors
Publication date: Available online 19 December 2019Source: Journal of Molecular Graphics and ModellingAuthor(s): Daniel M. Shadrack, Hulda S. Swai, Ali HassanaliAbstractMolecular chaperone Heat Shock Protein 90 (Hsp90) represents an interesting chemotherapeutic target for cancer treatments as it plays a role in cancer proliferation. Thus, continued effort to identify novel inhibitors of this target is an important task. Drug design using computational approach has gained significant attention in recent years. This work aims to propose docking protocols to re-purpose FDA-approved drugs targeting Hsp90. Sensitivity of result...
Source: Journal of Molecular Graphics and Modelling - December 20, 2019 Category: Molecular Biology Source Type: research

Complexation of peptide epitopes with G4-PAMAM dendrimer through ligand diffusion molecular dynamic simulations
Publication date: Available online 20 December 2019Source: Journal of Molecular Graphics and ModellingAuthor(s): Martiniano Bello, Rolando Alberto Rodríguez-Fonseca, José Correa-BasurtoAbstractPeptide epitopes from HIV-1 gp120 have been used to block the gp120-CD4 complex, whereas their poor absorbable or immunogenic properties prevent them from coupling to generation four polyamidoamine (PAMAM-G4) dendrimers. PAMAM-G4 are synthetic nanoparticles that are relatively nontoxic and nonimmunogenic have been employed as nanocarriers. In a previous study, two peptide epitopes (ABC and PGV04) from gp120 located at t...
Source: Journal of Molecular Graphics and Modelling - December 20, 2019 Category: Molecular Biology Source Type: research

A comparative study for the intermediate states of myelin oligodendrocyte glycoprotein in the absence and presence of glycan – A computational approach
Publication date: Available online 20 December 2019Source: Journal of Molecular Graphics and ModellingAuthor(s): Rita Mathews, L. RamyaAbstractMyelin Oligodendrocyte glycoprotein (MOG) is found to play an important role in providing structural integrity to myelin sheath at the same time it acts as an auto-antigen which might lead to Multiple Sclerosis (MS). What causes this specific property of being an auto-antigen is still not known. Here we present molecular dynamics simulation studies of unfolding and folding of the protein MOG in both the absence and presence of N-glycan in order to understand the role of glycosylatio...
Source: Journal of Molecular Graphics and Modelling - December 20, 2019 Category: Molecular Biology Source Type: research

A DFT study of Janus structure of S and Se in HfSSe layered as a promising candidate for electronic devices
Publication date: Available online 18 December 2019Source: Journal of Molecular Graphics and ModellingAuthor(s): M. Barhoumi, K. Lazaar, S. Bouzidi, M. SaidAbstractThe transition-metal dichalcogenides are presently being intensively researched because of their unique optoelectronic properties. Further, the success of TMDs in all areas of science without exception has opened the street to find other two-dimensional materials. Based on density functional theory, we study the vibrational and electronic properties of the mixed-phase of S and Se in HfSSe system, i.e, HfSSe monolayer and HfSSe/HfSSe bilayer. In this framework, o...
Source: Journal of Molecular Graphics and Modelling - December 20, 2019 Category: Molecular Biology Source Type: research

Unraveling the sequence of electron flows along the reaction mechanism by quantum topological tools: The 32CA reaction of acetonitrile oxide with 7-bromo-oxanorborn‐5‐en‐2‐one
Publication date: Available online 16 December 2019Source: Journal of Molecular Graphics and ModellingAuthor(s): Adjieufack Abel Idrice, Djogang Lucie Karelle, Lekene Ngouateu Rene Blaise, Mbah Bake Maraf, Nana Nouhou Cyrille, Emadak Alphonse, Ketcha Joseph Mbadcam, Mbouombouo Ndassa IbrahimAbstractThis work lays out the flow of electron density taking place along four reaction pathways of 32CA reaction of acetonitrile oxide between 7-bromo-oxanorborn‐5‐en‐2‐one has been examined in detail from the perspective in accordance with the bonding evolution theory (BET). The BET study makes apparent the non-concerted bond...
Source: Journal of Molecular Graphics and Modelling - December 17, 2019 Category: Molecular Biology Source Type: research

Theoretical study on prismatic (N6)n (n=16–35) molecules
Publication date: Available online 14 December 2019Source: Journal of Molecular Graphics and ModellingAuthor(s): Qian Guo, Bing He, Hongwei ZhouAbstractAs a continuation of our study on the stability of pure nitrogen molecules, twenty members of the (N6)n (n = 16–35) molecular sequence with D3h or D3d symmetry alternatively are studied in this work. The structures and energies are examined at the B3LYP/cc‒pvDZ computational level. “Natural Bond Orbital (NBO)” and “Atom In Molecule (AIM)” analyses are performed to investigate the bonding properties and the electronic topologies of the pri...
Source: Journal of Molecular Graphics and Modelling - December 14, 2019 Category: Molecular Biology Source Type: research

Molecular modeling assisted identification and biological evaluation of potent cathepsin S inhibitors
Publication date: Available online 12 December 2019Source: Journal of Molecular Graphics and ModellingAuthor(s): Sabahuddin Ahmad, Sudha Bhagwati, Sushil Kumar, Dibyendu Banerjee, Mohammad Imran SiddiqiAbstractCathepsin S (CatS) is one of the cysteinyl cathepsins widely studied for its clinical significance and found to be a promising therapeutic target for several diseases; to name a few is arthritis, allergic inflammation, cancer, diabetes, obesity, and cystic fibrosis. Elevated CatS level is a contributing factor for related disorders, and therefore among different strategies to regulate the activity of CatS, one is to ...
Source: Journal of Molecular Graphics and Modelling - December 13, 2019 Category: Molecular Biology Source Type: research