cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11719572
title: Identification of naturally originated molecules as γ-aminobutyric acid receptor antagonist

description: γ-aminobutyric acid, being a principle neuromediator in humans controlling the inhibition signals, acts on the ligand-gated pentameric type A receptors to transmit their response. Any dysfunction of these receptors leads to neurological disorders and mental illness. Benzodiazepine has been used extensively for the treatment of these disorders, which shows its effect by reducing the threshold concentration of γ-aminobutyric acid required to activate the receptor. Being a central nervous system depressant, benzodiazepine is also a common substance of abuse along with other recreational drugs that show affinity towards the benzodiazepine binding site. Flumazenil is considered the first line of treatment for the overdose of these substances, which competes with them to bind with the receptor having a higher binding affinity towards the receptor. Like most of the synthetic drugs, Flumazenil also has some side-effects associated with it. Here we focus our work towards finding specific naturally originated antagonist of the benzodiazepine binding site to suggest an alternative for Flumazenil by performing various computational analysis like docking experiments followed by simulations and molecular mechanics poisson-boltzmann surface area analysis. Molecular docking experiments filtered out four ligand molecules specific for the benzodiazepine binding site, namely, ligand-1,7,9 and 17. Further, molecular dynamics simulations showed ligand-17 to have stable conformation in the binding site as well as a lower binding free energy as compared to Flumazenil. Due to its natural origin, ligand-17 is supposed to have lower side effects; therefore, its backbone can be further explored to develop specific antagonists of benzodiazepines. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.11829675.v2
title: Carbon fullerene acts as potential lead molecule against prospective molecular targets of biofilm-producing multidrug-resistant <i>Acinetobacter baumanni</i> and <i>Pseudomonas aerugenosa</i>: computational modeling and MD simulation studies

description: This study aimed to screen putative drug targets associated with biofilm formation of multidrug-resistant <i>Acinetobacter baumannii</i> and <i>Pseudomonas areugenosa</i> and prioritize carbon nano-fullerene as potential lead molecule by structure-based virtual screening. Based on the functional role, 36 and 83 genes that are involved in biofilm formation of <i>A. baumannii</i> and <i>P. areugenosa</i> respectively were selected and metabolic network was computationally constructed. The genes that lack three-dimensional structures were predicted and validated. Carbon nano-fullerene selected as lead molecule and their drug-likeliness and pharmacokinetics properties were computationally predicted. The binding potential of carbon nano-fullerene toward selected drug targets was modeled and compared with the binding of conventional drugs, doripenem, and polymyxin-B with their usual targets. The stabilities of four best-docked complexes were confirmed by molecular dynamic (MD) simulation. This study suggested that selected genes demonstrated relevant interactions in the constructed metabolic pathways. Carbon fullerene exhibited significant binding abilities to most of the prioritized targets in comparison with the binding of last-resort antibiotics and their usual target. The four best ligand–receptor interactions predicted by molecular docking revealed that stability throughout MD simulation. Notably, carbon fullerene exhibited profound binding with outer membrane protein (OmpA) and ribonuclease-HII (rnhB) of <i>A. baumannii</i> and 2-heptyl-4(1H)-quinolone synthase (pqsBC) and chemotaxis protein (wspA) of <i>P. aeruginosa</i>. Thus, the current study suggested that carbon fullerene was probably used as potential lead molecules toward selected targets of <i>A. baumannii</i> and <i>P. aeruginosa</i> and the applied aspects probably scaled up to design promising lead molecules toward these pathogens. Communicated by Ramaswamy H. Sarma.
DOI: 10.6084/m9.figshare.11719572.v2
title: Identification of naturally originated molecules as γ-aminobutyric acid receptor antagonist

description: γ-aminobutyric acid, being a principle neuromediator in humans controlling the inhibition signals, acts on the ligand-gated pentameric type A receptors to transmit their response. Any dysfunction of these receptors leads to neurological disorders and mental illness. Benzodiazepine has been used extensively for the treatment of these disorders, which shows its effect by reducing the threshold concentration of γ-aminobutyric acid required to activate the receptor. Being a central nervous system depressant, benzodiazepine is also a common substance of abuse along with other recreational drugs that show affinity towards the benzodiazepine binding site. Flumazenil is considered the first line of treatment for the overdose of these substances, which competes with them to bind with the receptor having a higher binding affinity towards the receptor. Like most of the synthetic drugs, Flumazenil also has some side-effects associated with it. Here we focus our work towards finding specific naturally originated antagonist of the benzodiazepine binding site to suggest an alternative for Flumazenil by performing various computational analysis like docking experiments followed by simulations and molecular mechanics poisson-boltzmann surface area analysis. Molecular docking experiments filtered out four ligand molecules specific for the benzodiazepine binding site, namely, ligand-1,7,9 and 17. Further, molecular dynamics simulations showed ligand-17 to have stable conformation in the binding site as well as a lower binding free energy as compared to Flumazenil. Due to its natural origin, ligand-17 is supposed to have lower side effects; therefore, its backbone can be further explored to develop specific antagonists of benzodiazepines. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.11687409
title: N-arylnaphthylamines as inhibitors of human immunodeficiency virus integrase - lens epithelium-derived growth factor interactions: theoretical studies

description: Presented work reports a comprehensive theoretical study on the inhibitory nature of N-arylnaphthylamines in Human Immunodeficiency Virus Integrase (HIV IN) - Lens Epithelium-Derived Growth Factor (LEDGF/p75) complexes. Factors influencing the inhibition efficiency in AlphaScreen% assay are evaluated and explained through the structure- and ligand-based studies; including molecular docking, molecular dynamics calculations, and quantitative structure-activity relationship (QSAR) approach. It has been shown that N-arylnaphthylamines possess a wide variety of binding poses. Three QSAR models have been developed using structural descriptors and descriptors derived from docking calculations. The activity of untested N-arylnaphthylamines have been predicted using the most successful model. Proposed here technique could become a useful tool for ligand selection, accelerating the development of a new generation of anti-HIV medications. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.11687409.v2
title: N-arylnaphthylamines as inhibitors of human immunodeficiency virus integrase - lens epithelium-derived growth factor interactions: theoretical studies

description: Presented work reports a comprehensive theoretical study on the inhibitory nature of N-arylnaphthylamines in Human Immunodeficiency Virus Integrase (HIV IN) - Lens Epithelium-Derived Growth Factor (LEDGF/p75) complexes. Factors influencing the inhibition efficiency in AlphaScreen% assay are evaluated and explained through the structure- and ligand-based studies; including molecular docking, molecular dynamics calculations, and quantitative structure-activity relationship (QSAR) approach. It has been shown that N-arylnaphthylamines possess a wide variety of binding poses. Three QSAR models have been developed using structural descriptors and descriptors derived from docking calculations. The activity of untested N-arylnaphthylamines have been predicted using the most successful model. Proposed here technique could become a useful tool for ligand selection, accelerating the development of a new generation of anti-HIV medications. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.11687409.v1
title: N-arylnaphthylamines as inhibitors of Human Immunodeficiency Virus Integrase - Lens Epithelium-Derived Growth Factor interactions: Theoretical studies

description: Presented work reports a comprehensive theoretical study on the inhibitory nature of N-arylnaphthylamines in Human Immunodeficiency Virus Integrase (HIV IN) - Lens Epithelium-Derived Growth Factor (LEDGF/p75) complexes. Factors influencing the inhibition efficiency in AlphaScreen% assay are evaluated and explained through the structure- and ligand-based studies; including molecular docking, molecular dynamics calculations, and quantitative structure-activity relationship (QSAR) approach. It has been shown that N-arylnaphthylamines possess a wide variety of binding poses. Three QSAR models have been developed using structural descriptors and descriptors derived from docking calculations. The activity of untested N-arylnaphthylamines have been predicted using the most successful model. Proposed here technique could become a useful tool for ligand selection, accelerating the development of a new generation of anti-HIV medications.
DOI: 10.6084/m9.figshare.11887674
title: Hydration thermodynamics of cytosolic phospholipase A<sub>2</sub> GIVA predict its membrane-associated parts and its highly hydrated binding site

description: During biological events, the water molecules associated with the protein are re-oriented to adapt to the new conditions, inducing changes in the system’s free energy. The characterization of water structure and thermodynamics may facilitate the prediction of certain biological events, such as the binding of a ligand and the membrane-associated parts of a protein. In this computational study, we calculated the hydration thermodynamics of cytosolic phospholipase A<sub>2</sub> group IV (GIVA cPLA<sub>2</sub>) to study the hydration properties of the protein’s surface and binding pocket. Hydrophobicity scales and the Grid Inhomogeneous Solvation Theory (GIST) tool were employed for the calculations. The hydrophobic areas of the protein’s surface were predicted more accurately with the GIST method rather than with the hydrophobicity scales. Based on this, a model of the protein-membrane complex was constructed. In addition, the calculation revealed the highly hydrated binding pocket that further contribute to our understanding of the ligands’ binding. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.11687406.v2
title: Molecular docking and molecular dynamics simulation approach to screen natural compounds for inhibition of <i>Xanthomonas oryzae pv. Oryzae</i> by targeting peptide deformylase

description: <i>Xanthomonas oryzae pv. Oryzae (Xoo)</i> causes bacterial leaf blight (BLB) of rice which results in a huge loss in production. Many chemicals are used to control BLB disease. However, these chemicals are toxic to the environments, animals and human beings. Thus, there is a demand to discover potential and safe natural pesticides to manage BLB disease successfully. Therefore, we screened a library of phytochemicals of different plants having antibacterial activity by targeting Peptide Deformylase (PDF) of <i>Xoo</i> using <i>in silico</i> techniques. A library of 318 phytochemicals was prepared and subjected to rigid and flexible molecular docking against PDF followed by molecular dynamics simulation and free energy analysis of protein-ligand complexes. The results of virtual screening showed that 14 compounds from different plants have good binding energy as compare to reference molecule (3 R)-2,3-dihydro[1,3] thiazolo [3,2 a]benzimidazol-3-ol) (-7.7 kcal mol<sup>−1</sup>). Out of 14 hit compounds, eight compounds that were selected based on binding energy were analyzed by Molecular dynamic (MD) simulation. Analysis of MD simulation revealed that eight compounds namely; Bisdemethoxycurcumin, Rosmarinic acid, Piperanine, Dihydropiperlonguminine, Piperdardine, Dihydrocurcumin and Lonhumosides B achieved good stability during the 80 ns MD simulation at 300 K in term of the RMSD. Further, we calculated RMSF, RG, SASA, and interaction energy after 40 ns due to showing the stability of complexes. From our results, we conclude that these natural compounds could inhibit <i>Xoo</i> by targeting PDF receptor and can be used as potential bactericidal candidates against BLB disease of rice against <i>Xoo</i> and other bacteria. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.11687406
title: Molecular docking and molecular dynamics simulation approach to screen natural compounds for inhibition of <i>Xanthomonas oryzae pv. Oryzae</i> by targeting peptide deformylase

description: <i>Xanthomonas oryzae pv. Oryzae (Xoo)</i> causes bacterial leaf blight (BLB) of rice which results in a huge loss in production. Many chemicals are used to control BLB disease. However, these chemicals are toxic to the environments, animals and human beings. Thus, there is a demand to discover potential and safe natural pesticides to manage BLB disease successfully. Therefore, we screened a library of phytochemicals of different plants having antibacterial activity by targeting Peptide Deformylase (PDF) of <i>Xoo</i> using <i>in silico</i> techniques. A library of 318 phytochemicals was prepared and subjected to rigid and flexible molecular docking against PDF followed by molecular dynamics simulation and free energy analysis of protein-ligand complexes. The results of virtual screening showed that 14 compounds from different plants have good binding energy as compare to reference molecule (3 R)-2,3-dihydro[1,3] thiazolo [3,2 a]benzimidazol-3-ol) (-7.7 kcal mol<sup>−1</sup>). Out of 14 hit compounds, eight compounds that were selected based on binding energy were analyzed by Molecular dynamic (MD) simulation. Analysis of MD simulation revealed that eight compounds namely; Bisdemethoxycurcumin, Rosmarinic acid, Piperanine, Dihydropiperlonguminine, Piperdardine, Dihydrocurcumin and Lonhumosides B achieved good stability during the 80 ns MD simulation at 300 K in term of the RMSD. Further, we calculated RMSF, RG, SASA, and interaction energy after 40 ns due to showing the stability of complexes. From our results, we conclude that these natural compounds could inhibit <i>Xoo</i> by targeting PDF receptor and can be used as potential bactericidal candidates against BLB disease of rice against <i>Xoo</i> and other bacteria. Communicated by Ramaswamy H. Sarma
DOI: 10.5517/ccdc.csd.cc26wkvj
title: CCDC 2052288: Experimental Crystal Structure Determination

description: Related Article: Tadeusz Lis, Józef Utko|2020|CSD Communication|||
DOI: 10.5517/ccdc.csd.cc26wkxl
title: CCDC 2052290: Experimental Crystal Structure Determination

description: Related Article: Tadeusz Lis, Józef Utko|2020|CSD Communication|||
DOI: 10.5517/ccdc.csd.cc26wkym
title: CCDC 2052291: Experimental Crystal Structure Determination

description: Related Article: Tadeusz Lis, Józef Utko|2020|CSD Communication|||
DOI: 10.5517/ccdc.csd.cc26wl0q
title: CCDC 2052293: Experimental Crystal Structure Determination

description: Related Article: Tadeusz Lis, Józef Utko|2020|CSD Communication|||
DOI: 10.5517/ccdc.csd.cc26wl1r
title: CCDC 2052294: Experimental Crystal Structure Determination

description: Related Article: Zofia Janas, Tadeusz Lis|2020|CSD Communication|||
DOI: 10.5517/ccdc.csd.cc26wl2s
title: CCDC 2052295: Experimental Crystal Structure Determination

description: Related Article: Tadeusz Lis|2020|CSD Communication|||
DOI: 10.5517/ccdc.csd.cc9xd7t
title: CCDC 295406: Experimental Crystal Structure Determination

description: Related Article: Vijay Mahadevan, Peter Belser and Helen Stoeckli-Evans|2021|CSD Communication|||
DOI: 10.5517/ccdc.csd.cc26wmtk
title: CCDC 2052349: Experimental Crystal Structure Determination

description: Related Article: Robin Rogers|2020|CSD Communication|||
DOI: 10.5517/ccdc.csd.cc26wmvl
title: CCDC 2052350: Experimental Crystal Structure Determination

description: Related Article: Robin Rogers|2020|CSD Communication|||
DOI: 10.5517/ccdc.csd.cc26wmwm
title: CCDC 2052351: Experimental Crystal Structure Determination

description: Related Article: Robin Rogers|2020|CSD Communication|||
DOI: 10.5517/ccdc.csd.cc26wmxn
title: CCDC 2052352: Experimental Crystal Structure Determination

description: Related Article: Robin Rogers|2020|CSD Communication|||
DOI: 10.5517/ccdc.csd.cc26wn6z
title: CCDC 2052361: Experimental Crystal Structure Determination

description: Related Article: Robin Rogers|2020|CSD Communication|||
DOI: 10.5517/ccdc.csd.cc26wn70
title: CCDC 2052362: Experimental Crystal Structure Determination

description: Related Article: Robin Rogers|2020|CSD Communication|||
DOI: 10.5517/ccdc.csd.cc26wn81
title: CCDC 2052363: Experimental Crystal Structure Determination

description: Related Article: Robin Rogers|2020|CSD Communication|||
DOI: 10.5517/ccdc.csd.cc26wn92
title: CCDC 2052364: Experimental Crystal Structure Determination

description: Related Article: Robin Rogers|2020|CSD Communication|||
DOI: 10.5517/ccdc.csd.cc26wnb3
title: CCDC 2052365: Experimental Crystal Structure Determination

description: Related Article: Robin D. Rogers, Kevin H. Shaughnessy|2020|CSD Communication|||
DOI: 10.5517/ccdc.csd.cc26wnvm
title: CCDC 2052381: Experimental Crystal Structure Determination

description: Related Article: Robin D. Rogers, Michael P. Cava|2020|CSD Communication|||
DOI: 10.5517/ccdc.csd.cc26wnwn
title: CCDC 2052382: Experimental Crystal Structure Determination

description: Related Article: Robin D. Rogers, Michael P. Cava|2020|CSD Communication|||
DOI: 10.5517/ccdc.csd.cc26xcl3
title: CCDC 2053055: Experimental Crystal Structure Determination

description: Related Article: Ferdinand Belaj, Belina Terfassa, Jörg A. Schachner, Nadia C. Mösch-Zanetti|2020|CSD Communication|||
DOI: 10.5517/ccdc.csd.cc26xcm4
title: CCDC 2053056: Experimental Crystal Structure Determination

description: Related Article: Ferdinand Belaj, Martina E. Judmaier, Nadia C. Mösch-Zanetti|2020|CSD Communication|||
DOI: 10.5517/ccdc.csd.cc2667l8
title: CCDC 2031789: Experimental Crystal Structure Determination

description: Related Article: huchen huchen|2020|CSD Communication|||
description: Related Article: Chen Hu, Yingnan Zhao, Xiao Han, Jiaqi Song, Jie Ding, Hongwei Hou|2021|Dalton Trans.|50|1816|doi:10.1039/D0DT03817B
DOI: 10.5517/ccdc.csd.cc2667nb
title: CCDC 2031791: Experimental Crystal Structure Determination

description: Related Article: huchen huchen|2020|CSD Communication|||
description: Related Article: Chen Hu, Yingnan Zhao, Xiao Han, Jiaqi Song, Jie Ding, Hongwei Hou|2021|Dalton Trans.|50|1816|doi:10.1039/D0DT03817B
DOI: 10.5517/ccdc.csd.cc2667m9
title: CCDC 2031790: Experimental Crystal Structure Determination

description: Related Article: huchen huchen|2020|CSD Communication|||
description: Related Article: Chen Hu, Yingnan Zhao, Xiao Han, Jiaqi Song, Jie Ding, Hongwei Hou|2021|Dalton Trans.|50|1816|doi:10.1039/D0DT03817B
DOI: 10.5517/ccdc.csd.cc2667pc
title: CCDC 2031792: Experimental Crystal Structure Determination

description: Related Article: huchen huchen|2020|CSD Communication|||
description: Related Article: Chen Hu, Yingnan Zhao, Xiao Han, Jiaqi Song, Jie Ding, Hongwei Hou|2021|Dalton Trans.|50|1816|doi:10.1039/D0DT03817B
DOI: 10.5517/ccdc.csd.cc2667qd
title: CCDC 2031793: Experimental Crystal Structure Determination

description: Related Article: huchen huchen|2020|CSD Communication|||
description: Related Article: Chen Hu, Yingnan Zhao, Xiao Han, Jiaqi Song, Jie Ding, Hongwei Hou|2021|Dalton Trans.|50|1816|doi:10.1039/D0DT03817B
DOI: 10.15468/makjr6
title: On the taxonomic position of Indiacypridinae (Crustacea, Ostracoda), with the description of a new species of Indiacypris Hartmann, 1964 from Chalakkudy River (Kerala, India)

description: This dataset contains the digitized treatments in Plazi based on the original journal article George, Sunny, Martens, Koen (2004): On the taxonomic position of Indiacypridinae (Crustacea, Ostracoda), with the description of a new species of Indiacypris Hartmann, 1964 from Chalakkudy River (Kerala, India). Journal of Natural History 38 (5): 537-548, DOI: 10.1080/0022293021000013870, URL: http://www.tandfonline.com/doi/abs/10.1080/0022293021000013870
DOI: 10.3886/e113440v1-83520
title: Replication data for: Copyright Infringement in the Market for Digital Images

description: Digital technologies for sharing creative goods create new opportunities for copyright infringement and challenge established enforcement methods. We establish several important facts about the nature of copyright infringement and efforts to settle past infringing use in the market for digital images. Infringement in this, and many other markets, is often uninformed: users may be unaware that their use infringes, and may lack information about the price of a license. The uninformed nature of infringement implies that price may not be the primary factor in the decision to settle past use; in contrast, non-price factors may significantly affect settlement outcomes.
DOI: 10.5281/zenodo.4674308
title: Simulations of a pulmonary surfactant monolayer with additional compounds at higher concentrations

description: To be added... Topologies and mdp files available at <pre>https://doi.org/10.5281/zenodo.4627963</pre>
DOI: 10.5281/zenodo.4674307
title: Simulations of a pulmonary surfactant monolayer with additional compounds at higher concentrations

description: To be added... Topologies and mdp files available at <pre>https://doi.org/10.5281/zenodo.4627963</pre>
DOI: 10.6084/m9.figshare.14394269.v1
title: DistanceData_150321.xlsx

description: Distance Data underlying study by (Chitan et al.)
DOI: 10.6084/m9.figshare.14394269
title: DistanceData_150321.xlsx

description: Distance Data underlying study by (Chitan et al.)
DOI: 10.5281/zenodo.4675368
title: Dataset for "Direct Observation of Ultrafast Hydrogen Bond Strengthening in Liquid Water"

description: This is the dataset behind all the figures for the manuscript "Direct Observation of Ultrafast Hydrogen Bond Strengthening in Liquid Water".
DOI: 10.6084/m9.figshare.13194080
title: Relativistic Effects on Triple Black Hole Systems

description: Data for the influence of mass, distance, relativistic corrections on the evolution of triple black hole systems.
DOI: 10.6084/m9.figshare.13194080.v2
title: Relativistic Effects on Triple Black Hole Systems

description: Data for the influence of mass, distance, relativistic corrections on the evolution of triple black hole systems.
DOI: 10.6084/m9.figshare.13194080.v1
title: Relativistic Effects on Triple Black Hole Systems

description: Data for the influence of mass, distance, relativistic corrections on the evolution of triple black hole systems.
DOI: 10.34934/dvn/klbw5n
title: General Election Study Belgium 1991

description: General Election Survey Belgium (GESN) is a survey on the attitudes, opinions and political and social behaviour of Belgians, carried out after the federal elections of 24 November 1991. The data collected make it possible to measure the respondents' political information and knowledge, their perceptions of political bodies such as parties and social problems. Other issues include party identification, partisan preferences, representations of political efficacy, and the nature and extent of political participation. Perceptions of social class and (economic) welfare, authoritarianism, as well as attitudes towards immigrant workers, political corruption and the environment, are among the other areas studied in these surveys. Extensive demographic data on respondents was also collected. Translated with www.DeepL.com/Translator (free version)