cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.17896765.v2
title: Chemical Composition and Antibacterial Properties of Essential Oil Extracted from the Leaves and the Rhizomes of <i>Stahlianthus thorelii</i> Gagnep. (Zingiberaceae)

description: <i>Stahlianthus thorelii</i> Gagnep. is a plant belonging to the family Zingiberaceae, widely distributed in Asian countries like China, Thailand, India and Vietnam. In traditional oriental medicine, this plant is usually used to treat hemorrhage, heavy menstruation, poor digestion, rheumatism and bone / joint pain (tuberous roots). For the first time, the essential oils from the leaves and the rhizomes of <i>S. thorelii</i> collected in Vietnam were analyzed by Gas Chromatography-coupled with Mass Spectrometry (GC/MS) and investigated for their <i>in vitro</i> anti-microbacterial activity against several Gram (+) / (-) bacteria, fungi and yeast. A total of twenty and thirty components were detected accounting for 81.5 % and 95.5 % of the rhizome and leaf oils, respectively. These volatile compounds were identified as a complex of monoterpene fractions (14.2 % / 9.4 %) and mainly sesquiterpenes (60.0 % / 63.9 %) respectively. The most abundant sesquiterpenes in rhizome were found to be α-copaene (32.2 %) and (-)-<i>allo</i>-aromadendrene (11.3 %) while these compounds in leaves were identified only as 5.0 % and 5.3 %, respectively. In the antibacterial tests, the rhizome oil at MIC 150-200 μg/ml exhibited distinct activity against the Gram (+) bacteria <i>Bacillus subtilis</i>, <i>Staphylococcus aureus</i>, and the fungi <i>Aspergillus niger</i>. While the oil obtained from leaves at MIC 200 μg/ml showed inhibitory activity against <i>B. subtillis</i>.
DOI: 10.6084/m9.figshare.12936203.v1
title: SARS-CoV M<sup>pro</sup> inhibitory activity of aromatic disulfide compounds: QSAR model

description: The main protease (M<sup>pro</sup>) of SARS-associated coronavirus (SARS-CoV) had caused a high rate of mortality in 2003. Current events (2019–2020) substantiate important challenges for society due to coronaviruses. Consequently, advancing models for the antiviral activity of therapeutic agents is a necessary component of the fast development of treatment for the virus. An analogy between anti-SARS agents suggested in 2017 and anti-coronavirus COVID-19 agents are quite probable. Quantitative structure-activity relationships for SARS-CoV are developed and proposed in this study. The statistical quality of these models is quite good. Mechanistic interpretation of developed models is based on the statistical and probability quality of molecular alerts extracted from SMILES. The novel, designed structures of molecules able to possess anti-SARS activities are suggested. For the final assessment of the designed molecules inhibitory potential, developed from the obtained QSAR model, molecular docking studies were applied. Results obtained from molecular docking studies were in a good correlation with the results obtained from QSAR modeling. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.12981944.v1
title: Phthalocyanine complexes with (4-isopropylbenzyl)oxy substituents: preparation and evaluation of anti-carbonic anhydrase, anticholinesterase enzymes and molecular docking studies

description: In this study, the preparation, aggregation behavior and investigation of carbonic anhydrase and cholinesterase enzyme inhibition features of non-peripherally (4-isopropylbenzyl)oxy-substituted phthalocyanines (<b>4–6</b>) are reported for the first time. The chemical structures of these new phthalocyanines were elucidated by UV-Vis (ultraviolet-visible), FT-IR (Fourier transform infrared spectrometry), NMR (nuclear magnetic resonance) and MALDI-TOF (matrix-assisted laser desorption/ionization time-of-flight) mass spectrometry. The substitution of 4-isopropylbenzyl)oxy groups benefits a remarkable solubility and redshift of the phthalocyanines Q-band. Also, these complexes were tested against some enzymes such as butyrylcholinesterase enzyme, human carbonic anhydrase I and II isoforms and acetylcholinesterase enzyme. The phthalocyanine complexes showed Ki values of in the range of 478.13 ± 57.25–887.25 ± 101.20 µM against hCA I, 525.16 ± 45.87–921.14 ± 81.25 µM against hCA II, 68.33 ± 9.13–201.15 ± 35.86 µM against AChE and 86.25 ± 13.65–237.54 ± 24.7 µM against BChE. Molecular docking studies were performed to investigate the binding modes and interaction energies of the (<b>2–6</b>) complexes with the hCA I (PDB ID:1BMZ), hCA II (PDB ID:2ABE), AChE (PDB ID:4EY6) and BChE (PDB ID:2PM8). Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.12981944
title: Phthalocyanine complexes with (4-isopropylbenzyl)oxy substituents: preparation and evaluation of anti-carbonic anhydrase, anticholinesterase enzymes and molecular docking studies

description: In this study, the preparation, aggregation behavior and investigation of carbonic anhydrase and cholinesterase enzyme inhibition features of non-peripherally (4-isopropylbenzyl)oxy-substituted phthalocyanines (<b>4–6</b>) are reported for the first time. The chemical structures of these new phthalocyanines were elucidated by UV-Vis (ultraviolet-visible), FT-IR (Fourier transform infrared spectrometry), NMR (nuclear magnetic resonance) and MALDI-TOF (matrix-assisted laser desorption/ionization time-of-flight) mass spectrometry. The substitution of 4-isopropylbenzyl)oxy groups benefits a remarkable solubility and redshift of the phthalocyanines Q-band. Also, these complexes were tested against some enzymes such as butyrylcholinesterase enzyme, human carbonic anhydrase I and II isoforms and acetylcholinesterase enzyme. The phthalocyanine complexes showed Ki values of in the range of 478.13 ± 57.25–887.25 ± 101.20 µM against hCA I, 525.16 ± 45.87–921.14 ± 81.25 µM against hCA II, 68.33 ± 9.13–201.15 ± 35.86 µM against AChE and 86.25 ± 13.65–237.54 ± 24.7 µM against BChE. Molecular docking studies were performed to investigate the binding modes and interaction energies of the (<b>2–6</b>) complexes with the hCA I (PDB ID:1BMZ), hCA II (PDB ID:2ABE), AChE (PDB ID:4EY6) and BChE (PDB ID:2PM8). Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.12936203
title: SARS-CoV M<sup>pro</sup> inhibitory activity of aromatic disulfide compounds: QSAR model

description: The main protease (M<sup>pro</sup>) of SARS-associated coronavirus (SARS-CoV) had caused a high rate of mortality in 2003. Current events (2019–2020) substantiate important challenges for society due to coronaviruses. Consequently, advancing models for the antiviral activity of therapeutic agents is a necessary component of the fast development of treatment for the virus. An analogy between anti-SARS agents suggested in 2017 and anti-coronavirus COVID-19 agents are quite probable. Quantitative structure-activity relationships for SARS-CoV are developed and proposed in this study. The statistical quality of these models is quite good. Mechanistic interpretation of developed models is based on the statistical and probability quality of molecular alerts extracted from SMILES. The novel, designed structures of molecules able to possess anti-SARS activities are suggested. For the final assessment of the designed molecules inhibitory potential, developed from the obtained QSAR model, molecular docking studies were applied. Results obtained from molecular docking studies were in a good correlation with the results obtained from QSAR modeling. Communicated by Ramaswamy H. Sarma
DOI: 10.5281/zenodo.5612430
title: Data supporting "Slowest-first translation scheme: Structural asymmetry along protein sequences and co-translational folding"

description: Contains data for a set of 16,200 non-redundant protein structures taken from the Protein Data Bank. Associated code can be found at https://github.com/jomimc/FoldAsymCode.
DOI: 10.6084/m9.figshare.12978298.v1
title: <i>In silico</i> drug discovery of IKK-β inhibitors from 2-amino-3-cyano-4-alkyl-6-(2-hydroxyphenyl) pyridine derivatives based on QSAR, docking, molecular dynamics and drug-likeness evaluation studies

description: The Inhibitor of IKK-β (nuclear factor kappa B kinase subunit beta), a specific modulator of NF-κB (nuclear factor-κB), is considered a valid target to discover new active compounds for various cancers and rheumatoid arthritis treatment. In this study a series of thirty 2-amino-3-cyano-4-alkyl-6-(2-hydroxyphenyl) pyridine derivatives was involved for a quantitative structure activity relationship model (QSAR) elaboration which allows the prediction of the pIC50 values of new designed compounds. The model can be used to predict the activity of new compounds within its applicability domain. Then a molecular docking study was carried out to identify the interactions between the compounds and the amino acids of the active site. After that, golden triangle, Veber’s rule, and Lipinski’s rule properties were calculated to identify the drug-likeness properties of the investigated compounds. Finally, in-silico-toxicity studies were performed to predict the toxicity of the new designed compounds. The analysis of the results of QSAR model and molecular docking succeeded to screen 21 interesting compounds with better inhibitory concentration having a good affinity to IKK-β. All compounds were within the range set by Veber’s rule and Lipinski’s rule. the analysis of golden triangle showed that the thirty 2-amino-3-cyano-4-alkyl-6-(2-hydroxyphenyl) pyridine derivatives would not have clearance and cell membrane permeability problems except comp6 comp12,comp20, comp21, and comp26.As for the new designed compounds, their properties may have these problems, except two compounds which are: A8m, A8p. The A1m, A1p, A3p and A11m compounds were predicted to be nontoxic. These findings indicate that the novel potent candidate drugs have promising potential to IKK-β enzyme inhibition and should motivate future experimental investigations. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.12978298
title: <i>In silico</i> drug discovery of IKK-β inhibitors from 2-amino-3-cyano-4-alkyl-6-(2-hydroxyphenyl) pyridine derivatives based on QSAR, docking, molecular dynamics and drug-likeness evaluation studies

description: The Inhibitor of IKK-β (nuclear factor kappa B kinase subunit beta), a specific modulator of NF-κB (nuclear factor-κB), is considered a valid target to discover new active compounds for various cancers and rheumatoid arthritis treatment. In this study a series of thirty 2-amino-3-cyano-4-alkyl-6-(2-hydroxyphenyl) pyridine derivatives was involved for a quantitative structure activity relationship model (QSAR) elaboration which allows the prediction of the pIC50 values of new designed compounds. The model can be used to predict the activity of new compounds within its applicability domain. Then a molecular docking study was carried out to identify the interactions between the compounds and the amino acids of the active site. After that, golden triangle, Veber’s rule, and Lipinski’s rule properties were calculated to identify the drug-likeness properties of the investigated compounds. Finally, in-silico-toxicity studies were performed to predict the toxicity of the new designed compounds. The analysis of the results of QSAR model and molecular docking succeeded to screen 21 interesting compounds with better inhibitory concentration having a good affinity to IKK-β. All compounds were within the range set by Veber’s rule and Lipinski’s rule. the analysis of golden triangle showed that the thirty 2-amino-3-cyano-4-alkyl-6-(2-hydroxyphenyl) pyridine derivatives would not have clearance and cell membrane permeability problems except comp6 comp12,comp20, comp21, and comp26.As for the new designed compounds, their properties may have these problems, except two compounds which are: A8m, A8p. The A1m, A1p, A3p and A11m compounds were predicted to be nontoxic. These findings indicate that the novel potent candidate drugs have promising potential to IKK-β enzyme inhibition and should motivate future experimental investigations. Communicated by Ramaswamy H. Sarma
DOI: 10.5281/zenodo.5612429
title: Data supporting "Slowest-first translation scheme: Structural asymmetry along protein sequences and co-translational folding"

description: Contains data for a set of 16,200 non-redundant protein structures taken from the Protein Data Bank. Associated code can be found at https://github.com/jomimc/FoldAsymCode.
DOI: 10.6084/m9.figshare.12932703.v1
title: Screening natural inhibitors against upregulated G-protein coupled receptors as potential therapeutics of Alzheimer’s disease

description: Computational approaches have been helpful in high throughput screening of drug libraries and designing ligands against receptors. Alzheimer's disease is a complex neurological disorder, which causes dementia. In this disease neurons are damaged due to formation of Amyloid-beta plaques and neurofibrillary tangles, which along with some other factors contributes to disease development and progression. The objective of this study was to predict tertiary structures of five G-protein coulped neurotransmitter receptors; CHRM5, CYSLTR2, DRD5, GALR1 and HTR2C, that are upregulated in Alzheimer’s disease, and to screen potential inhibitors for against these receptors. In this study, Comparative modelling, molecular docking, MMGBSA analysis, ADMET screening and molecular dynamics simulation were performed. Tertiary structures of the five GPCRs were predicted and further subjected to molecular docking against natural compounds. Pharmacokinetic studies of natural compounds were also conducted for assessing drug-likeness properties. Molecular dynamics simulations were performed to investigate the structural stability and binding affinities of each complex. Finally, the results suggested that ZINC04098704, ZINC31170017, ZINC05998597, ZINC67911229, and ZINC67910690 had better binding affinity with CHRM5, CYSLTR2, DRD5, GALR1, and HTR2C (5-HT2C) proteins, respectively. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.12932703
title: Screening natural inhibitors against upregulated G-protein coupled receptors as potential therapeutics of Alzheimer’s disease

description: Computational approaches have been helpful in high throughput screening of drug libraries and designing ligands against receptors. Alzheimer's disease is a complex neurological disorder, which causes dementia. In this disease neurons are damaged due to formation of Amyloid-beta plaques and neurofibrillary tangles, which along with some other factors contributes to disease development and progression. The objective of this study was to predict tertiary structures of five G-protein coulped neurotransmitter receptors; CHRM5, CYSLTR2, DRD5, GALR1 and HTR2C, that are upregulated in Alzheimer’s disease, and to screen potential inhibitors for against these receptors. In this study, Comparative modelling, molecular docking, MMGBSA analysis, ADMET screening and molecular dynamics simulation were performed. Tertiary structures of the five GPCRs were predicted and further subjected to molecular docking against natural compounds. Pharmacokinetic studies of natural compounds were also conducted for assessing drug-likeness properties. Molecular dynamics simulations were performed to investigate the structural stability and binding affinities of each complex. Finally, the results suggested that ZINC04098704, ZINC31170017, ZINC05998597, ZINC67911229, and ZINC67910690 had better binding affinity with CHRM5, CYSLTR2, DRD5, GALR1, and HTR2C (5-HT2C) proteins, respectively. Communicated by Ramaswamy H. Sarma
DOI: 10.17632/44m6rzdmv2.2
title: Data for “Modeling rainfall-infiltration-runoff processes on sloping surfaces subject to rapidly changing soil hydraulic properties during seal formation”

description: The dataset includes the simulated and observed data for “Modeling rainfall-infiltration-runoff processes on sloping surfaces subject to rapidly changing soil hydraulic properties during seal formation”.
DOI: 10.15151/esrf-es-644087617
title: Proteins and protein/DNA/RNA complexes involved in biosynthesis, protein folding and degradation, splicing, cancer, host pathogen interacti
DOI: 10.15151/esrf-es-644087871
title: SAARLAND BAG: ATOMIC MECHANISMS OF ACTION OF MEMBRANE PROTEINS AND BIOSYNTHETIC ENZYMES

description: Projects are focussed primarily within the framework of the DFG-funded excellence network program on "Ca2+signals: Molecular Mechanisms und Integrative Functions" at Saarland University and a new joint multidisciplinary initiative of the University with the Helmholtz Institute of Pharmaceutical Research Saarland on natural bioactive compounds including their interactions with their target proteins. These projects involve the structure determination of membrane proteins and soluble proteins.
DOI: 10.15151/esrf-es-644088239
title: Austrian Crystallographic Diffraction Consortium

description: This proposed Austrian Crystallographic Diffraction Consortium (ACDC) BAG is to support various macromolecular structural biology groups across Austria (totally 15 research groups at 8 institutions in 5 cities). We employ mainly the technique of X-ray crystallography to characterize macromolecular biological complexes. Approval of this BAG will be absolutely essential for researchers in all these groups to carry out their structural studies on various health-related subjects, which are targeted at characterizing large molecular assemblies or proteins currently under-represented in the PDB, including membrane proteins. Corresponding high-resolution diffraction data are only obtainable through the use of synchrotron radiation sources. Thus regular synchrotron access is highly desirable to maintain a competitive advantage in our individual research fields.
DOI: 10.17632/msdkfsvxbm.1
title: F21020022

description: Referensi Jurnal UAS PTIK Semester 1 tahun 2022
DOI: 10.15151/esrf-es-645947945
title: Study of the degradation of Cadmium Yellow in historical and historically reconstructed oil paints

description: This proposal concerns the study of the composition and degradation of Cadmium Yellow (CdY) oil paints in relation to the historical synthesis methods of the pigment. Although the degradation mechanism of CdY paints has been elucidated, it has been demonstrated that not all CdY paints show the same extent of degradation. This fact can be related to the use of different historical synthesis methods, which influence the pigment properties and could induce a different reactivity of the pigment. We propose to characterize through µ-XRF/µ-XANES analysis the chemical speciation and stratigraphic distribution of compounds in artificially aged CdY model paints prepared with pigments synthesized by different historical methods, to provide a quantitative assessment of the degree of degradation in relation with the manufacturing process. The research will complement the study of historical paint samples from original CdY degraded paintings, to compare artificial degradation with real one.
DOI: 10.15151/esrf-es-646796246
title: Local distortions in new rare-earth-free oxygen-ion conductor

description: We propose a high-temperature diffraction study of a newly synthesised oxygen-ion conductor material. The compound is stable as a cubic Pm-3m perovskite structure, but has a structured of mass loss through the compositional range at moderate temperatures. A multiple-temperature Pair-Distribution Function analysis study of this material will provide valuable insights on the mechanism of local distortions and vacancy order/disorder that are likely to be behind this exceptional behaviour. A full characterisation will allow to bring this promising low-temperature oxygen ion conductor forward for applications as a cathode in new generation solid-oxide fuel cells, more environmentally friendly and affordable
DOI: 10.17632/t5dyns635c.1
title: Moh Adib Jauhar PTIK UAS

description: Mencari jurnal penelitian sesuai intruksi Dari bapak bosen
DOI: 10.15151/esrf-es-642970891
title: Evolution of the shark skeleton

description: Comparative jawed-vertebrate hard-tissue microstructural dataset.
DOI: 10.15151/esrf-es-642971437
title: Bacterial membrane rupture mechanism by biodegradable Gemini surfactants

description: Biodegradable Gemini surfactants are dimeric surfactants incorporating hydrolysable moieties into their hydrophobic constituents. They combine enhanced antimicrobial efficacy with biodegradability, giving potential for industrial formulation in personal care products. However, their dynamic interactions with the bacterial membrane are not well understood. In collaboration with P&G, the world’s largest personal care product manufacturer, we propose to investigate the dynamic interactions between biodegradable Gemini surfactants with bacteria-mimicking liposomes comprising DDPE, DPPG and cardiolipin (CL). We will use time-resolved USAXS/SAXS/WAXS combined with rapid stopped-flow mixing to study the effects of surfactant binding on the dynamic structure of liposomes and the structural order of phospholipid chains . The results will provide mechanistic insights into the interactions between the biodegradable moieties of these novel Gemini surfactants and membranes.
DOI: 10.15151/esrf-es-658528198
title: High-energy Bragg coherent diffraction imaging during an electrochemical reaction

description: We intend to follow and study the structural changes in three dimensions (3D) of multiple Pt nanoparticles (NPs) under realistic electrochemical reactions, such as oxygen reduction reaction (ORR) and hydrogen evolution reaction (HER). More precisely, we aim to map the strain response of multiple single NPs as a function of the electrode potential by probing the particles with BCDI at high energy. The Pt NPs will be immersed in H2SO4 and the electrode potential will be applied to trigger different reactions (e.g ORR, HER).
DOI: 10.15151/esrf-es-642438092
title: Local atomic structure in Cd-Mg-Tb quasicrystals by x-ray fluorescence holography

description: The aim of this proposal is to use X-ray fluorescence holography experiments to provide insight into the positional and chemical disorder of an icosahedral quasicrystal and an appoximant crystal in the Cd-Mg-Tb system. This technique provides unique advantages as a tool to investigate the structure of quasicrystals, particularly because it can directly visualize the local 3-dimensional atomic scale structure in physical space, without being impeded by the phase problem of traditional crystallography. The setup for this experiment is well established, and preliminary computer simulations have already been performed to establish a reference frame for the experimental results.
DOI: 10.15151/esrf-es-641834023
title: In situ sulphur poisoning and regeneration of Cu-CHA deNOx catalysts

description: Excellent performance of Cu-exchanged chabazite zeolites (Cu-CHA) as catalysts for NOx removal from exhaust fumes has very recently paved the way for these materials to the catalytic converters of the last-generation diesel cars. However, catalytic activity of these materials decreases after prolonged exposure to sulphur, ever-present in the diesel fuel. To understand the mechanism of deactivation we need to investigate Cu-S species which are formed after interaction with SO2. This proposal aims to reveal the mechanisms of sulphur poisoning and regeneration of Cu-CHA zeolites at the molecular level, monitoring the electronic structure and local environment of sulphur by element-selective X-ray absorption spectroscopy during the in situ adsorption and desorption of sulphur. Obtained results will be crucial to optimise regeneration procedures for the catalysts, increasing thus their efficiency.
DOI: 10.15151/esrf-es-663184212
title: Silicon calibration

description: Silicon calibration