cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.4415126
title: Datasets associated with Agostini, S., Houlbreque, F., Biscéré, T., Harvey, B. P., Heitzman, J. M., Takimoto, R., et al. (2020). Greater mitochondrial energy production provides resistance to ocean acidification in 'winning' hermatypic corals. Front. Mar. Sci. 7. doi:10.3389/fmars.2020.600836.

description: Datasets associated with Agostini, S., Houlbreque, F., Biscéré, T., Harvey, B. P., Heitzman, J. M., Takimoto, R., et al. (2020). Greater mitochondrial energy production provides resistance to ocean acidification in ‘winning’ hermatypic corals. Front. Mar. Sci. 7. doi:10.3389/fmars.2020.600836.
DOI: 10.5517/ccdc.csd.cc1q6y2y
title: CCDC 1585590: Experimental Crystal Structure Determination

description: Related Article: Wen-Min Wang, Lei Huai, Xi-Wen Wang, Kai-Jun Jiang, Hai-Yun Shen, Hong-Ling Gao, Ming Fang, Jian-Zhong Cui|2020|New J.Chem.|44|10266|doi:10.1039/D0NJ01969K
description: Related Article: Jia Ji, Kai-Jun Jiang, Hai-Yun Shen, Yan Tian, Yin-Ling Hou, Hong-Ling Gao, Wen-Min Wang, Jian-Zhong Cui|2021|J.Mol.Struct.|1228|129753|doi:10.1016/j.molstruc.2020.129753
DOI: 10.6084/m9.figshare.13515998
title: dat2.zip

description: The column name represents the TCGA ID, and the row name represents the gene symbol.<br>
DOI: 10.6084/m9.figshare.13515998.v1
title: dat2.zip

description: The column name represents the TCGA ID, and the row name represents the gene symbol.<br>
DOI: 10.34777/jqrp-ea30
title: FERET-Morphs

description: Description : FERET-Morphs is a dataset of morphed face images generated by applying different landmark and generative adversarial networks techniques on the FERET dataset.
DOI: 10.5281/zenodo.4415211
title: Lost in Zero Space -- An Empirical Comparison of 0.y.z Releases in Four Software Package Distributions

description: <pre>The notebooks in "notebooks/" require the dependencies specified in "requirements.txt" to be installed. They rely on data files in "data/". These data can be obtained by running the "convert.py" scripts in that folder. The script requires data files from "data-raw/". These files can be generated by running "extract.py" in that folder. This script requires the libraries.io data dump, as explained in the README file contained in this folder. If you don't have these data, or if you don't want to download them, you can ask for the required data/*.csv.gz files by email.</pre>
DOI: 10.5281/zenodo.4013419
title: Lost in Zero Space -- An Empirical Comparison of 0.y.z Releases in Four Software Package Distributions

description: <pre>The notebooks in "notebooks/" require the dependencies specified in "requirements.txt" to be installed. They rely on data files in "data/". These data can be obtained by running the "convert.py" scripts in that folder. The script requires data files from "data-raw/". These files can be generated by running "extract.py" in that folder. This script requires the libraries.io data dump, as explained in the README file contained in this folder. If you don't have these data, or if you don't want to download them, you can ask for the required data/*.csv.gz files by email.</pre>
DOI: 10.34777/vypt-sz23
title: FRGC-Morphs

description: Description : FRGC-Morphs is a dataset of morphed face images generated by applying different landmark and generative adversarial networks techniques on the FRGC dataset.
DOI: 10.6084/m9.figshare.11636487
title: Effect of tetracycline family of antibiotics on actin aggregation, resulting in the formation of Hirano bodies responsible for neuropathological disorders

description: Actin, an ATPase superfamily protein, regulates some vital biological functions like cell locomotion, cytokinesis, synaptic plasticity and cell signaling in higher eukaryotes, and is dependent on the dynamics of actin polymerization process. Impaired regulation of actin polymerization has been implicated in the formation and deposition of rod-like paracrystalline structures called as Hirano bodies in neuronal cells of patients suffering from Alzheimer’s disease, Pick’s disease, Guam amyotrophic lateral sclerosis and parkinsonism–dementia complex. Aggregation of actin forming amorphous deposition in the brain cells is also associated with chronic alcoholism and aging of the neurons. In the current article, we propose the breaking of the highly amorphous and dysregulated actin aggregates using generic compounds like tetracycline, oxytetracycline, doxycycline and minocycline which are used as antibiotics against tuberculosis and infection caused due to various Gram-negative bacteria. We have investigated the effect and affinity of binding of these four compounds to that of actin aggregates using 90° light scattering, size exclusion chromatography, dynamic light scattering, circular dichroism, scanning electron microscopy, transmission electron microscopy imaging and kinetic analysis. The isothermal calorimetric measurements showed that the binding constant for the cycline family molecules used in this study range from 9.8 <i>E</i>4 M<sup>−1</sup> to 1.3 <i>E</i>4 M<sup>−1</sup>. To understand the <i>in vivo</i> effect, we also studied the effect of these drugs on <i>Saccharomyces cerevisiae</i> Δ<i>end3</i> mutant cells. Our data suggest that these generic compounds can plausibly be used for the treatment of various neurodegenerative diseases occurring due to Hirano body formation in brain cells. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.11448072
title: Exploring the different states of wild-type T-cell receptor and mutant conformational changes towards understanding the antigen recognition

description: Recognition of proteolytic peptide fragments presented by major histocompatibility complex (MHC) on target cells by T-cell receptor (TCR) is among the most important interactions in the adaptive immune system. Several computational studies have been performed to investigate conformational and dynamical properties of TCRs for enhanced immunogenicity. Here, we present the large-scale molecular dynamics (MD) simulation studies of the two comprehensive systems consisting of the wild-type and mutant IG4 TCR in complex with the tumor epitope NY-ESO peptide (SLLMWITQC) and analyzed for mapping conformational changes of TCR in the states prior to antigen binding, upon antigen binding and after the antigen was released. All of the simulations were performed with different states of TCRs for each 1000 ns of simulation time, providing six simulations for time duration of 6000 ns (6µs). We show that rather than undergoing most critical conformational changes upon antigen binding, the high proportion of complementarity-determining region (CDR) loops change by comparatively small amount. The hypervariable CDRα3 and CDRβ3 loops showed significant structural changes. Interestingly, the TCR β chain loops showed the least changes, which is reliable with recent implications that β domain of TCR may propel antigen interaction. The mutant shows higher rigidity than wild-type even in released state; expose an induced fit mechanism occurring from the re-structuring of CDRα3 loop and can allow enhanced binding affinity of the peptide antigen. Additionally, we show that CDRα3 loop and peptide contacts are an adaptive feature of affinity enhanced mutant TCR. Communicated by Ramaswamy H. Sarma The wild-type has sampled significantly larger conformational changes than the mutant even in the released state.
DOI: 10.6084/m9.figshare.11448072.v2
title: Exploring the different states of wild-type T-cell receptor and mutant conformational changes towards understanding the antigen recognition

description: Recognition of proteolytic peptide fragments presented by major histocompatibility complex (MHC) on target cells by T-cell receptor (TCR) is among the most important interactions in the adaptive immune system. Several computational studies have been performed to investigate conformational and dynamical properties of TCRs for enhanced immunogenicity. Here, we present the large-scale molecular dynamics (MD) simulation studies of the two comprehensive systems consisting of the wild-type and mutant IG4 TCR in complex with the tumor epitope NY-ESO peptide (SLLMWITQC) and analyzed for mapping conformational changes of TCR in the states prior to antigen binding, upon antigen binding and after the antigen was released. All of the simulations were performed with different states of TCRs for each 1000 ns of simulation time, providing six simulations for time duration of 6000 ns (6µs). We show that rather than undergoing most critical conformational changes upon antigen binding, the high proportion of complementarity-determining region (CDR) loops change by comparatively small amount. The hypervariable CDRα3 and CDRβ3 loops showed significant structural changes. Interestingly, the TCR β chain loops showed the least changes, which is reliable with recent implications that β domain of TCR may propel antigen interaction. The mutant shows higher rigidity than wild-type even in released state; expose an induced fit mechanism occurring from the re-structuring of CDRα3 loop and can allow enhanced binding affinity of the peptide antigen. Additionally, we show that CDRα3 loop and peptide contacts are an adaptive feature of affinity enhanced mutant TCR. Communicated by Ramaswamy H. Sarma The wild-type has sampled significantly larger conformational changes than the mutant even in the released state.
DOI: 10.6084/m9.figshare.11448099
title: Identification of potential inhibitors against pathogenic missense mutations of PMM2 using a structure-based virtual screening approach

description: The autosomal recessive phosphomannomutase 2-congenital disorder of glycosylation (PMM2-CDG) is characterized by defective functioning of the PMM2 enzyme, which is necessary for the conversion of mannose-6-phosphate into mannose-1-phosphate. Here, a computational pipeline was drawn to identify the most significant mutations, and further, we used a virtual screening approach to identify a new lead compound to treat the identified significant mutations. We searched for missense mutation data related to PMM2-CDG in HGMD®, UniProt, and ClinVar. Our search yielded a total of 103 mutations, of which 91 are missense mutations. The D65Y, I132N, I132T, and F183S mutations were classified as deleterious, destabilizing, and altering the biophysical properties using the PredictSNP, iStable, and Align GVGD <i>in silico</i> prediction tools. Additionally, we applied a multistep protocol to screen for an alternative lead compound to the existing CID2876053 (1-(3-chlorophenyl)-3,3-bis(pyridine-2-yl)urea) with affinity to these identified significant mutants. Two compounds, CHEMBL1491007 (6-chloro-4-phenyl-3-(4-pyridin-2-ylpiperazin-1-yl)-1H-quinolin-2-one) and CHEMBL3653029 (5-chloro-4-[6-[(3-fluorophenyl)methylamino]pyridin-2-yl]-N-(piperidin-4-ylmethyl)pyridin-2-amine), exhibited the highest binding affinity with the selected mutants and were chosen for further analysis. Through molecular docking, molecular dynamics simulation, and MMPBSA analysis, we found that the known compound, i.e. CID2876053, has stronger interaction with the D65Y mutant. The newly identified lead compound CHEMBL1491007 showed stronger interaction with the I132N and I132T mutants, whereas the most deleterious mutant, F183S, showed stronger interaction with CHEMBL3653029. This study is expected to aid in the field of precision medicine, and further to <i>in vivo</i> and <i>in vitro</i> analysis of these lead compounds might shed light on the treatment of PMM2-CDG. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.11448099.v2
title: Identification of potential inhibitors against pathogenic missense mutations of PMM2 using a structure-based virtual screening approach

description: The autosomal recessive phosphomannomutase 2-congenital disorder of glycosylation (PMM2-CDG) is characterized by defective functioning of the PMM2 enzyme, which is necessary for the conversion of mannose-6-phosphate into mannose-1-phosphate. Here, a computational pipeline was drawn to identify the most significant mutations, and further, we used a virtual screening approach to identify a new lead compound to treat the identified significant mutations. We searched for missense mutation data related to PMM2-CDG in HGMD®, UniProt, and ClinVar. Our search yielded a total of 103 mutations, of which 91 are missense mutations. The D65Y, I132N, I132T, and F183S mutations were classified as deleterious, destabilizing, and altering the biophysical properties using the PredictSNP, iStable, and Align GVGD <i>in silico</i> prediction tools. Additionally, we applied a multistep protocol to screen for an alternative lead compound to the existing CID2876053 (1-(3-chlorophenyl)-3,3-bis(pyridine-2-yl)urea) with affinity to these identified significant mutants. Two compounds, CHEMBL1491007 (6-chloro-4-phenyl-3-(4-pyridin-2-ylpiperazin-1-yl)-1H-quinolin-2-one) and CHEMBL3653029 (5-chloro-4-[6-[(3-fluorophenyl)methylamino]pyridin-2-yl]-N-(piperidin-4-ylmethyl)pyridin-2-amine), exhibited the highest binding affinity with the selected mutants and were chosen for further analysis. Through molecular docking, molecular dynamics simulation, and MMPBSA analysis, we found that the known compound, i.e. CID2876053, has stronger interaction with the D65Y mutant. The newly identified lead compound CHEMBL1491007 showed stronger interaction with the I132N and I132T mutants, whereas the most deleterious mutant, F183S, showed stronger interaction with CHEMBL3653029. This study is expected to aid in the field of precision medicine, and further to <i>in vivo</i> and <i>in vitro</i> analysis of these lead compounds might shed light on the treatment of PMM2-CDG. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.11522211
title: Structural and functional alterations of nitric oxide synthase 3 due to missense variants associate with high-altitude pulmonary edema through dynamic study

description: The human endothelial nitric oxide synthase (<i>NOS3</i>) is 28 Kbp at 7q36.1 and encodes protein comprising of 1280 amino acids. Being a major source of nitric oxide, the enzyme is crucial to the vascular homeostasis and thereby to be an important pharmaceutical target. We hence have been investigating this molecule in a high-altitude disorder namely, high-altitude pulmonary edema (HAPE). We performed a genome-wide association study (GWAS) in a case-control design of sojourners that included healthy controls and HAPE patients (<i>n</i> = 200) each. Four <i>NOS3</i> missense SNPs i.e. rs1799983 (E298D), rs3918232 (V827M), rs3918201 (R885M) and rs3918234 (Q982L), were associated significantly with HAPE (<i>P</i>-value &lt; 0.05). Furthermore, extensive <i>in silico</i> analyses were performed to predict the detrimental effect of the four variant types and their three most relevant co-factors namely, heme, flavin adenine dinucleotide (FAD) and flavin mononucleotide (FMN) that are accountable for amendment of protein stability leading to structural de-construction. Subsequently, we validated the findings in a larger sample size of the two study groups. HAPE patients had a higher frequency of the four variants and significantly decreased levels of circulating nitric oxide (NO) (<i>P</i>-value &lt; 0.001). The <i>in silico</i> and human subjects findings complement each other. This study explored the impact of HAPE-associated <i>NOS3</i> variants with its protein structure stability and holds promise to be current and future drug targets. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.11448066
title: Observation of quantum signature in rivastigmine chemical bond break-up and quantum energetics, spectral studies of anti-Alzheimer inhibitors

description: Semi-empirical calculations on the torsion potential for dihedral angle of rivastigmine linking NAP and Carbamyle moieties consistently show regions of several discontinuities and a cusp indicating molecular instability and eventual break-up of rivastigmine observed in the X-ray structure. The phenomena can be explained both by definition of large classical force or quantum nature of chemical bond break-up. Also, to better understand the molecular properties and quantum energetics of the inhibitor molecules, we have performed several ab initio based calculations on all four inhibitors at equilibrium geometry, in ground state and gas phase using the density functional theory level wB97X/6-31G* and HF/6-31G*. A number of properties like computational vibrational (IR), Raman and nuclear magnetic resonance (NMR) spectra as well as HOMO and LUMO orbital energies at optimized geometries have been computed by SPARTAN16 and Gaussian16 utilities. Also, the thermodynamic and QSAR properties of the inhibitors have been assessed and compared by a number of different semi-quantum, Hartree-Fock and density functional methods. The theoretical NMR and IR spectra have been benchmarked against experimental spectrum to compare and assess suitability of the computational methodologies and basis set levels for the calculations. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.11506809
title: Cellular prion protein gene polymorphisms linked to differential scrapie susceptibility correlate with distinct residue connectivity between secondary structure elements

description: The conformational conversion of the cellular prion protein (PrP<sup>C</sup>) to the misfolded and aggregated isoform, termed scrapie prion protein (PrP<sup>Sc</sup>), is key to the development of a group of neurodegenerative diseases known as transmissible spongiform encephalopathies (TSEs). Although the conversion mechanism is not fully understood, the role of gene polymorphisms in varying susceptibilities to prion diseases is well established. In ovine, specific gene polymorphisms in PrP<sup>C</sup> alter prion disease susceptibility: the Valine136–Glutamine171 variant (<i>Susceptible</i> structure) displays high susceptibility to classical scrapie while the Alanine136–Arginine171 variant (<i>Resistant</i> structure) displays reduced susceptibility. The opposite trend has been reported in atypical scrapie. Despite the differentiation between classical and atypical scrapie, a complete understanding of the effect of polymorphisms on the structural dynamics of PrP<sup>C</sup> is lacking. From our structural bioinformatics study, we propose that polymorphisms locally modulate the network of residue interactions in the globular C-terminus of the ovine recombinant prion protein while maintaining the overall fold. Although the two variants we examined exhibit a densely connected group of residues that includes both β-sheets, the β2–α2 loop and the N-terminus of α-helix 2, only in the <i>Resistant</i> structure do most residues of α-helix 2 belong to this group. We identify the structural role of Valine136Alanine and Glutamine171Arginine: modulation of residue interaction networks that affect the connectivity between α-helix 2 and α-helix 3. We propose blocking interactions of residue 171 as a potential target for the design of therapeutics to prevent efficient PrP<sup>C</sup> misfolding. We discuss our results in the context of initial PrP<sup>C</sup> conversion and extrapolate to recently proposed PrP<sup>Sc</sup> structures. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.11506809.v2
title: Cellular prion protein gene polymorphisms linked to differential scrapie susceptibility correlate with distinct residue connectivity between secondary structure elements

description: The conformational conversion of the cellular prion protein (PrP<sup>C</sup>) to the misfolded and aggregated isoform, termed scrapie prion protein (PrP<sup>Sc</sup>), is key to the development of a group of neurodegenerative diseases known as transmissible spongiform encephalopathies (TSEs). Although the conversion mechanism is not fully understood, the role of gene polymorphisms in varying susceptibilities to prion diseases is well established. In ovine, specific gene polymorphisms in PrP<sup>C</sup> alter prion disease susceptibility: the Valine136–Glutamine171 variant (<i>Susceptible</i> structure) displays high susceptibility to classical scrapie while the Alanine136–Arginine171 variant (<i>Resistant</i> structure) displays reduced susceptibility. The opposite trend has been reported in atypical scrapie. Despite the differentiation between classical and atypical scrapie, a complete understanding of the effect of polymorphisms on the structural dynamics of PrP<sup>C</sup> is lacking. From our structural bioinformatics study, we propose that polymorphisms locally modulate the network of residue interactions in the globular C-terminus of the ovine recombinant prion protein while maintaining the overall fold. Although the two variants we examined exhibit a densely connected group of residues that includes both β-sheets, the β2–α2 loop and the N-terminus of α-helix 2, only in the <i>Resistant</i> structure do most residues of α-helix 2 belong to this group. We identify the structural role of Valine136Alanine and Glutamine171Arginine: modulation of residue interaction networks that affect the connectivity between α-helix 2 and α-helix 3. We propose blocking interactions of residue 171 as a potential target for the design of therapeutics to prevent efficient PrP<sup>C</sup> misfolding. We discuss our results in the context of initial PrP<sup>C</sup> conversion and extrapolate to recently proposed PrP<sup>Sc</sup> structures. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.11522211.v2
title: Structural and functional alterations of nitric oxide synthase 3 due to missense variants associate with high-altitude pulmonary edema through dynamic study

description: The human endothelial nitric oxide synthase (<i>NOS3</i>) is 28 Kbp at 7q36.1 and encodes protein comprising of 1280 amino acids. Being a major source of nitric oxide, the enzyme is crucial to the vascular homeostasis and thereby to be an important pharmaceutical target. We hence have been investigating this molecule in a high-altitude disorder namely, high-altitude pulmonary edema (HAPE). We performed a genome-wide association study (GWAS) in a case-control design of sojourners that included healthy controls and HAPE patients (<i>n</i> = 200) each. Four <i>NOS3</i> missense SNPs i.e. rs1799983 (E298D), rs3918232 (V827M), rs3918201 (R885M) and rs3918234 (Q982L), were associated significantly with HAPE (<i>P</i>-value &lt; 0.05). Furthermore, extensive <i>in silico</i> analyses were performed to predict the detrimental effect of the four variant types and their three most relevant co-factors namely, heme, flavin adenine dinucleotide (FAD) and flavin mononucleotide (FMN) that are accountable for amendment of protein stability leading to structural de-construction. Subsequently, we validated the findings in a larger sample size of the two study groups. HAPE patients had a higher frequency of the four variants and significantly decreased levels of circulating nitric oxide (NO) (<i>P</i>-value &lt; 0.001). The <i>in silico</i> and human subjects findings complement each other. This study explored the impact of HAPE-associated <i>NOS3</i> variants with its protein structure stability and holds promise to be current and future drug targets. Communicated by Ramaswamy H. Sarma
DOI: 10.5519/qd.1kof3bmf
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (38 records)
DOI: 10.5519/qd.dfte3pnp
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (13 records)
DOI: 10.5519/qd.a4l8t75k
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (1 records)
DOI: 10.5519/qd.f4mbmbwj
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (1 records)
DOI: 10.5519/qd.pwmybl5d
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (3 records)