cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.6836889
title: TrypTag: plate A1697 (replicate dated 20160106)

description: TrypTag genome-wide protein localisation project data. Widefield epifluorescence microscope images of protein subcellular localisation in the unicellular eukaryotic pathogen <i>Trypanosoma brucei</i> by endogenous tagging with mNeonGreen (mNG). Raw microscopy data and per-cell line localisation annotation for plate A1697, replicate dated 20160106.
DOI: 10.5281/zenodo.7065646
title: TrypTag: plate A1697 (replicate dated 20160106)

description: TrypTag genome-wide protein localisation project data. Widefield epifluorescence microscope images of protein subcellular localisation in the unicellular eukaryotic pathogen <i>Trypanosoma brucei</i> by endogenous tagging with mNeonGreen (mNG). Raw microscopy data and per-cell line localisation annotation for plate A1697, replicate dated 20160106.
DOI: 10.21227/152a-cm06
title: Gesture dataset

description: Including the improved yolov model training data set and the collected gesture coordinates to draw the graph
DOI: 10.5281/zenodo.6840752
title: TrypTag: plate L3530 (replicate dated 20170209)

description: TrypTag genome-wide protein localisation project data. Widefield epifluorescence microscope images of protein subcellular localisation in the unicellular eukaryotic pathogen <i>Trypanosoma brucei</i> by endogenous tagging with mNeonGreen (mNG). Raw microscopy data and per-cell line localisation annotation for plate L3530, replicate dated 20170209.
DOI: 10.24403/jp.1246431
title: Winterexkursion der Thüringischen Botanischen Gesellschaft zu unterschiedlichen Laubwaldtypen im Mittleren Saaletal bei Jena am 22. Februar 2014 : Führung: Frank H. Hellwig (Kahla), Jörn Hentschel (Jena) und Heiko Korsch (Jena) / Peter Rode (Stadtroda)
DOI: 10.24403/jp.1246432
title: Kurzer Bericht über die Exkursion der Thüringischen Botanischen Gesellschaft in den Südostteil des Kyffhäusergebirges am 27. August 2016 : Führung: Jürgen Pusch (Bad Frankenhausen) / Peter Rode (Stadtroda)
DOI: 10.5281/zenodo.7065186
title: TrypTag: plate 327054 (replicate dated 20170406)

description: TrypTag genome-wide protein localisation project data. Widefield epifluorescence microscope images of protein subcellular localisation in the unicellular eukaryotic pathogen <i>Trypanosoma brucei</i> by endogenous tagging with mNeonGreen (mNG). Raw microscopy data and per-cell line localisation annotation for plate 327054, replicate dated 20170406.
DOI: 10.5281/zenodo.6835359
title: TrypTag: plate 327054 (replicate dated 20170406)

description: TrypTag genome-wide protein localisation project data. Widefield epifluorescence microscope images of protein subcellular localisation in the unicellular eukaryotic pathogen <i>Trypanosoma brucei</i> by endogenous tagging with mNeonGreen (mNG). Raw microscopy data and per-cell line localisation annotation for plate 327054, replicate dated 20170406.
DOI: 10.24403/jp.1246434
title: Exkursion der Thüringischen Botanischen Gesellschaft in den „Pfaffenbachsgrund südlich Rodacherbrunn“ am 30. Juni 2018 : Führung: Hans-Christian Schmidt (Weida) und Ralf Schmiede (Erfurt) / Peter Rode (Stadtroda)
DOI: 10.6084/m9.figshare.21081166
title: Kim_Johns_CatMirrorSelfRecognition_Data

description: KIM Youngbean and Philip JOHNS. Using online media to assess mirror self-recognition in domestic cats <br> Data used for BORIS analysis of sequential behaviours and of behavioural clusters.
DOI: 10.6084/m9.figshare.14179054.v1
title: Structural insight into the binding interactions of NTPs and nucleotide analogues to RNA dependent RNA polymerase of SARS-CoV-2

description: RNA dependent RNA polymerase (RdRP) from positive-stranded RNA viruses has always been a hot target for designing of new drugs. Major class of drugs that are targeted against RdRP are nucleotide analogues. Extensive docking and molecular dynamics study describing the binding of natural nucleotides (NTPs) and its analogues leading to significant structural variation in the RdRP has been presented here. RdRP simulations in its apo, NTP-bound, and analogue-bound form have been performed. Nucleotide analogues included in this study were, favipiravir, galidesivir, lamivudine, ribavirin, remdesivir and sofosbuvir. The conformational flexibility of the RdRP molecule has been explored using principal component (PCA) and Markov state modeling (MSM) analysis. PCA inferred the presence of correlated motions among the conserved motifs of RdRP. Inter-domain distances between the finger and thumb subdomain flanking the nascent RNA template entry site sampled open and closed conformations. The ligand and template binding motifs F and G showed negatively correlated motions. K551, R553, and R555, a part of motif F appear to form strong interactions with the ligand molecules. R836, a primer binding residue was observed to strongly bind to the analogues. MSM analysis helped to extract statistically distinct conformations explored by the RdRP. Ensemble docking of the ligands on the Markov states also suggested the involvement of the above residues in ligand interactions. Markov states obtained clearly demarcated the open/closed conformations of the template entry site. These observations on residues from the conserved motifs involved in binding to the ligands may provide an insight into designing new inhibitors. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.14206589
title: Potential inhibitors of angiotensin converting enzyme 2 receptor of COVID-19 by <i>Corchorus olitorius</i> Linn using docking, molecular dynamics, conceptual DFT investigation and pharmacophore mapping

description: A novel coronavirus, previously designated 2019-nCoV, was identified as the cause of a cluster of pneumonia cases in Wuhan, a city in the Hubei Province of China, at the end of 2019. Our objective focuses on the in silico study to screen for an alternative drug that can block the activity of the angiotensin converting enzyme 2 (ACE2), which is a key protein in the physiology of Covid-19, necessary for the entry of the SARS-Cov-2 virus into the host's cells using natural compounds especially phenolic antioxidants, polyphenolics and pharmaceutically phytochemicals derived from the leaves of <i>Corchorus olitorius</i> Linn, appear to be very potential in controlling virus-induced infection. The results of the docking simulation revealed that méthyl-1,4,5-tri-O-caféoyl quinate has a stronger bond, high affinity and gives the best docking scores compared to, the co-crystallized inhibitor (PRD_002214) of the enzyme ACE2, chloroquine, hydroxychloroquine, captopril and simerprevir antiviral drugs. The ADMET properties, Pharmacokinetics and Medicinal Chemistry & P450 site of metabolism prediction, pharmacophore Mapper enzyme revealed that the compound méthyl-1,4,5-tri-O-caféoyl quinate generates a hypothesis which can be applied successfully in biological screening for further experiments. The novel MD computational technique study showed better conformational movements result for the méthyl-1,4,5-tri-O-caféoyl quinate-ACE2 docked complex. Therefore méthyl-1,4,5-tri-O-caféoyl quinate may be considered to be potential inhibitor of the main protease enzyme of virus, but need to be investigated <i>in vivo</i> and <i>in vitro</i> for further drug development process. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.14206589.v1
title: Potential inhibitors of angiotensin converting enzyme 2 receptor of COVID-19 by <i>Corchorus olitorius</i> Linn using docking, molecular dynamics, conceptual DFT investigation and pharmacophore mapping

description: A novel coronavirus, previously designated 2019-nCoV, was identified as the cause of a cluster of pneumonia cases in Wuhan, a city in the Hubei Province of China, at the end of 2019. Our objective focuses on the in silico study to screen for an alternative drug that can block the activity of the angiotensin converting enzyme 2 (ACE2), which is a key protein in the physiology of Covid-19, necessary for the entry of the SARS-Cov-2 virus into the host's cells using natural compounds especially phenolic antioxidants, polyphenolics and pharmaceutically phytochemicals derived from the leaves of <i>Corchorus olitorius</i> Linn, appear to be very potential in controlling virus-induced infection. The results of the docking simulation revealed that méthyl-1,4,5-tri-O-caféoyl quinate has a stronger bond, high affinity and gives the best docking scores compared to, the co-crystallized inhibitor (PRD_002214) of the enzyme ACE2, chloroquine, hydroxychloroquine, captopril and simerprevir antiviral drugs. The ADMET properties, Pharmacokinetics and Medicinal Chemistry & P450 site of metabolism prediction, pharmacophore Mapper enzyme revealed that the compound méthyl-1,4,5-tri-O-caféoyl quinate generates a hypothesis which can be applied successfully in biological screening for further experiments. The novel MD computational technique study showed better conformational movements result for the méthyl-1,4,5-tri-O-caféoyl quinate-ACE2 docked complex. Therefore méthyl-1,4,5-tri-O-caféoyl quinate may be considered to be potential inhibitor of the main protease enzyme of virus, but need to be investigated <i>in vivo</i> and <i>in vitro</i> for further drug development process. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.14179054
title: Structural insight into the binding interactions of NTPs and nucleotide analogues to RNA dependent RNA polymerase of SARS-CoV-2

description: RNA dependent RNA polymerase (RdRP) from positive-stranded RNA viruses has always been a hot target for designing of new drugs. Major class of drugs that are targeted against RdRP are nucleotide analogues. Extensive docking and molecular dynamics study describing the binding of natural nucleotides (NTPs) and its analogues leading to significant structural variation in the RdRP has been presented here. RdRP simulations in its apo, NTP-bound, and analogue-bound form have been performed. Nucleotide analogues included in this study were, favipiravir, galidesivir, lamivudine, ribavirin, remdesivir and sofosbuvir. The conformational flexibility of the RdRP molecule has been explored using principal component (PCA) and Markov state modeling (MSM) analysis. PCA inferred the presence of correlated motions among the conserved motifs of RdRP. Inter-domain distances between the finger and thumb subdomain flanking the nascent RNA template entry site sampled open and closed conformations. The ligand and template binding motifs F and G showed negatively correlated motions. K551, R553, and R555, a part of motif F appear to form strong interactions with the ligand molecules. R836, a primer binding residue was observed to strongly bind to the analogues. MSM analysis helped to extract statistically distinct conformations explored by the RdRP. Ensemble docking of the ligands on the Markov states also suggested the involvement of the above residues in ligand interactions. Markov states obtained clearly demarcated the open/closed conformations of the template entry site. These observations on residues from the conserved motifs involved in binding to the ligands may provide an insight into designing new inhibitors. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.14316026
title: Anti-glycemic potential of benzophenone thio/semicarbazone derivatives: synthesis, enzyme inhibition and ligand docking studies

description: Inhibition of dipeptidyl peptidase-IV (DPP-IV) has been identified as a promising approach for the treatment of type 2 diabetes mellitus (T2DM). Therefore, development of DPP-IV inhibitors with new chemical scaffold is of utmost importance to medicinal chemistry. In the present study, we identified benzophenone thio- and semicarbazone scaffolds as novel DPP-IV inhibitors. For that purpose, benzophenone thio- and semicarbazone were synthesized through a 2-step reaction. These newly synthetic derivatives were characterized by different spectroscopic techniques, including HREI-MS and NMR. whereas stereochemistry of the iminic bond was predicted by NOESY experiments. Thio- and semicarbazones derivatives were evaluated for their DPP-IV inhibitory potential and found to exhibit a good to moderate enzyme inhibitory activity. Most active and non-cytotoxic derivatives were further evaluated for their DPP-IV inhibitory potential in <i>in cellulo</i> model. The binding sites as well as affinity of active compounds for DPP- IV enzyme were predicted by <i>in silico</i> studies, and compared to a standard drug, sitagliptin. Pharmacophore studies of thio- and semicarbazones derivatives 1–29 suggest that substitution of aryl group, particularly a lipophilic substituents at C-4″ of benzene ring, and a hydroxyl at C-4′ strongly influenced the DPP-IV inhibitory activity. Compound 9 showed the highest inhibitory activity (IC<sub>50</sub> = 15.0 ± 0.6 µM), whereas compounds 10, 17, 12, 14 and 23 showed a moderate activity with IC<sub>50</sub> values in the range of 28.9–39.2 µM. This study identifies thio- and semicarbazones as new classes of DPP-IV inhibitors which may translate into safe and effective therapeutics for a better management of type 2 diabetes. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.14316026.v1
title: Anti-glycemic potential of benzophenone thio/semicarbazone derivatives: synthesis, enzyme inhibition and ligand docking studies

description: Inhibition of dipeptidyl peptidase-IV (DPP-IV) has been identified as a promising approach for the treatment of type 2 diabetes mellitus (T2DM). Therefore, development of DPP-IV inhibitors with new chemical scaffold is of utmost importance to medicinal chemistry. In the present study, we identified benzophenone thio- and semicarbazone scaffolds as novel DPP-IV inhibitors. For that purpose, benzophenone thio- and semicarbazone were synthesized through a 2-step reaction. These newly synthetic derivatives were characterized by different spectroscopic techniques, including HREI-MS and NMR. whereas stereochemistry of the iminic bond was predicted by NOESY experiments. Thio- and semicarbazones derivatives were evaluated for their DPP-IV inhibitory potential and found to exhibit a good to moderate enzyme inhibitory activity. Most active and non-cytotoxic derivatives were further evaluated for their DPP-IV inhibitory potential in <i>in cellulo</i> model. The binding sites as well as affinity of active compounds for DPP- IV enzyme were predicted by <i>in silico</i> studies, and compared to a standard drug, sitagliptin. Pharmacophore studies of thio- and semicarbazones derivatives 1–29 suggest that substitution of aryl group, particularly a lipophilic substituents at C-4″ of benzene ring, and a hydroxyl at C-4′ strongly influenced the DPP-IV inhibitory activity. Compound 9 showed the highest inhibitory activity (IC<sub>50</sub> = 15.0 ± 0.6 µM), whereas compounds 10, 17, 12, 14 and 23 showed a moderate activity with IC<sub>50</sub> values in the range of 28.9–39.2 µM. This study identifies thio- and semicarbazones as new classes of DPP-IV inhibitors which may translate into safe and effective therapeutics for a better management of type 2 diabetes. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.14191374
title: Insights into the interaction dynamics between volatile anesthetics and tubulin through computational molecular modelling

description: General anesthetics, able to reversibly suppress all conscious brain activity, have baffled medical science for decades, and little is known about their exact molecular mechanism of action. Given the recent scientific interest in the exploration of microtubules as putative functional targets of anesthetics, and the involvement thereof in neurodegenerative disorders, the present work focuses on the investigation of the interaction between human tubulin and four volatile anesthetics: ethylene, desflurane, halothane and methoxyflurane. Interaction sites on different tubulin isotypes are predicted through docking, along with an estimate of the binding affinity ranking. The analysis is expanded by Molecular Dynamics simulations, where the dimers are allowed to freely interact with anesthetics in the surrounding medium. This allowed for the determination of interaction hotspots on tubulin dimers, which could be linked to different functional consequences on the microtubule architecture, and confirmed the weak, Van der Waals-type interaction, occurring within hydrophobic pockets on the dimer. Both docking and MD simulations highlighted significantly weaker interactions of ethylene, consistent with its far lower potency as a general anesthetic. Overall, simulations suggest a transient interaction between anesthetics and microtubules in general anesthesia, and contact probability analysis shows interaction strengths consistent with the potencies of the four compounds. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.14191374.v1
title: Insights into the interaction dynamics between volatile anesthetics and tubulin through computational molecular modelling

description: General anesthetics, able to reversibly suppress all conscious brain activity, have baffled medical science for decades, and little is known about their exact molecular mechanism of action. Given the recent scientific interest in the exploration of microtubules as putative functional targets of anesthetics, and the involvement thereof in neurodegenerative disorders, the present work focuses on the investigation of the interaction between human tubulin and four volatile anesthetics: ethylene, desflurane, halothane and methoxyflurane. Interaction sites on different tubulin isotypes are predicted through docking, along with an estimate of the binding affinity ranking. The analysis is expanded by Molecular Dynamics simulations, where the dimers are allowed to freely interact with anesthetics in the surrounding medium. This allowed for the determination of interaction hotspots on tubulin dimers, which could be linked to different functional consequences on the microtubule architecture, and confirmed the weak, Van der Waals-type interaction, occurring within hydrophobic pockets on the dimer. Both docking and MD simulations highlighted significantly weaker interactions of ethylene, consistent with its far lower potency as a general anesthetic. Overall, simulations suggest a transient interaction between anesthetics and microtubules in general anesthesia, and contact probability analysis shows interaction strengths consistent with the potencies of the four compounds. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.14216327
title: Newly synthesized (R)-carvone-derived 1,2,3-triazoles: structural, mechanistic, cytotoxic and molecular docking studies

description: In the current study, natural (R)-carvone was used as starting material for the efficient synthesis of several 1,2,3-triazole derivatives. The produced products were obtained in good yields and characterized by <sup>1</sup>H and <sup>13</sup>C NMR and HRMS analysis. The newly synthesized monoterpenic 1,2,3-triazole <b>4</b> and derivatives were analyzed by viability tests (MTT) for their cytotoxic activity against three human cancer cells. Product <b>5</b> showed a medium antitumor activity, for which the IC<sub>50</sub> values against selected cells HT-1080, A-549 and MCF-7 were 29.25 μM, 31.62 μM and 26.02 μM, respectively. The regioselectivity of the condensation reaction and the molecular structure of the title compounds were determined by Density Functional Theory (DFT) using B3LYP calculations at 6-311 + G(d,p) level. The orbitals HOMO and LUMO were studied to determine the electronic properties of the synthesized compounds. In addition, the global reactivity indices were used to explain the regioselectivity for the formation of compound <b>6</b>, and the theoretical results agree well with the experimental results. Molecular docking and molecular dynamics confirmed the empirical test results and confirmed the stability of the complex during inhibition of the anti-apoptotic protein for killing cancer cells. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.14216327.v1
title: Newly synthesized (R)-carvone-derived 1,2,3-triazoles: structural, mechanistic, cytotoxic and molecular docking studies

description: In the current study, natural (R)-carvone was used as starting material for the efficient synthesis of several 1,2,3-triazole derivatives. The produced products were obtained in good yields and characterized by <sup>1</sup>H and <sup>13</sup>C NMR and HRMS analysis. The newly synthesized monoterpenic 1,2,3-triazole <b>4</b> and derivatives were analyzed by viability tests (MTT) for their cytotoxic activity against three human cancer cells. Product <b>5</b> showed a medium antitumor activity, for which the IC<sub>50</sub> values against selected cells HT-1080, A-549 and MCF-7 were 29.25 μM, 31.62 μM and 26.02 μM, respectively. The regioselectivity of the condensation reaction and the molecular structure of the title compounds were determined by Density Functional Theory (DFT) using B3LYP calculations at 6-311 + G(d,p) level. The orbitals HOMO and LUMO were studied to determine the electronic properties of the synthesized compounds. In addition, the global reactivity indices were used to explain the regioselectivity for the formation of compound <b>6</b>, and the theoretical results agree well with the experimental results. Molecular docking and molecular dynamics confirmed the empirical test results and confirmed the stability of the complex during inhibition of the anti-apoptotic protein for killing cancer cells. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.14259914
title: Molecular interaction study of novel indoline derivatives with EGFR-kinase domain using multiple computational analysis

description: Epidermal growth factor receptors are constitutively overexpressed in breast cancer cells, which in turn stimulate many downstream signaling pathways that are involved in many carcinogenic processes. This makes EGFR a striking target for cancer therapy. This study focuses on the EGFR kinase domain inactivation by novel synthesized indoline derivatives. The compounds used are N-(2-hydroxy-5-nitrophenyl (4’-methyl phenyl) methyl) indoline (HNPMI), alkylaminophenols − 2-((3,4-Dihydroquinolin-1(2H)-yl) (p-tolyl) methyl) phenol (THTMP) and 2-((1, 2, 3, 4-Tetrahydroquinolin-1-yl) (4 methoxyphenyl) methyl) phenol (THMPP). To get a clear insight into the molecular interaction of EGFR and the three compounds, we have used ADME/Tox prediction, Flexible docking analysis followed by MM/GB-SA, QM/MM analysis, E-pharmacophore mapping of the ligands and Molecular dynamic simulation of protein-ligand complexes. All three compounds showed good ADME/Tox properties obeying the rules of drug-likeliness and showed high human oral absorption. Molecular docking was performed with the compounds and EGFR using Glide Flexible docking mode. This showed that the HNPMI was best among the three compounds and had interactions with key residue Lys 721. The protein-ligand complexes were stable when simulated for 100 ns using Desmond software. The interactions were further substantiated using QM/MM analysis and MM-GB/SA analysis in which HNPMI was scored as the best molecule. All the analyses were carried out with a reference molecule—Gefitinib which is a known standard inhibitor of EGFR. Thus, the study elucidates the potential role of the indoline derivatives as an anti-cancer agent against breast cancer by effectively inhibiting EGFR. Communicated by Ramaswamy H. Sarma