cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.13233939
title: Identification of natural inhibitors against prime targets of SARS-CoV-2 using molecular docking, molecular dynamics simulation and MM-PBSA approaches

description: The recently emerged COVID-19 has been declared a pandemic by the World Health Organization as to date; no therapeutic drug/vaccine is available for the treatment. Due to the lack of time and the urgency to contain the pandemic, computational screening appears to be the best tool to find a therapeutic solution. Accumulated evidence suggests that many phyto-compounds possess anti-viral activity. Therefore, we identified possible phyto-compounds that could be developed and used for COVID-19 treatment. In particular, molecular docking was used to prioritize the possible active phyto-compounds against two key targets namely RNA dependent RNA polymerase (RdRp) and main protease (M<sup>pro</sup>) of SARS-CoV-2. In this study, an antiviral drug- Remdesivir (RdRp inhibitor) and Darunavir (M<sup>pro</sup> inhibitor) are used as reference drugs. This study revealed that phyto-molecules- Mulberroside-A/C/E/F, Emblicanin A, Nimbolide, and Punigluconin showed high binding affinity against RdRp while Andrographolides, Mulberrosides, Anolignans, Chebulic acid, Mimusopic acid, and Punigluconin showed better binding affinity against M<sup>pro</sup> as compared with the reference drug. Furthermore, ADME profiles validated the drug-likeness properties of prioritized phyto-compounds. Besides, to assess the stability, MD simulations studies were performed along with reference inhibitors for M<sup>pro</sup> (Darunavir) and RdRp (Remdesivir). Binding free energy calculations (MM-PBSA) revealed the estimated value (ΔG) of M<sup>pro</sup>_Darunavir; M<sup>pro</sup>_Mulberroside E; RdRp_Remdesivir and RdRp_Emblicanin A were −111.62 ± 6.788, −141.443 ± 9.313, 30.782 ± 5.85 and −89.424 ± 3.130 kJmol<sup>−1</sup>, respectively. Taken together, the study revealed the potential of these phyto-compounds as inhibitors of RdRp and M<sup>pro</sup> inhibitor that could be further validated against SARS-CoV-2 for clinical benefits. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.13233939.v1
title: Identification of natural inhibitors against prime targets of SARS-CoV-2 using molecular docking, molecular dynamics simulation and MM-PBSA approaches

description: The recently emerged COVID-19 has been declared a pandemic by the World Health Organization as to date; no therapeutic drug/vaccine is available for the treatment. Due to the lack of time and the urgency to contain the pandemic, computational screening appears to be the best tool to find a therapeutic solution. Accumulated evidence suggests that many phyto-compounds possess anti-viral activity. Therefore, we identified possible phyto-compounds that could be developed and used for COVID-19 treatment. In particular, molecular docking was used to prioritize the possible active phyto-compounds against two key targets namely RNA dependent RNA polymerase (RdRp) and main protease (M<sup>pro</sup>) of SARS-CoV-2. In this study, an antiviral drug- Remdesivir (RdRp inhibitor) and Darunavir (M<sup>pro</sup> inhibitor) are used as reference drugs. This study revealed that phyto-molecules- Mulberroside-A/C/E/F, Emblicanin A, Nimbolide, and Punigluconin showed high binding affinity against RdRp while Andrographolides, Mulberrosides, Anolignans, Chebulic acid, Mimusopic acid, and Punigluconin showed better binding affinity against M<sup>pro</sup> as compared with the reference drug. Furthermore, ADME profiles validated the drug-likeness properties of prioritized phyto-compounds. Besides, to assess the stability, MD simulations studies were performed along with reference inhibitors for M<sup>pro</sup> (Darunavir) and RdRp (Remdesivir). Binding free energy calculations (MM-PBSA) revealed the estimated value (ΔG) of M<sup>pro</sup>_Darunavir; M<sup>pro</sup>_Mulberroside E; RdRp_Remdesivir and RdRp_Emblicanin A were −111.62 ± 6.788, −141.443 ± 9.313, 30.782 ± 5.85 and −89.424 ± 3.130 kJmol<sup>−1</sup>, respectively. Taken together, the study revealed the potential of these phyto-compounds as inhibitors of RdRp and M<sup>pro</sup> inhibitor that could be further validated against SARS-CoV-2 for clinical benefits. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.13273103
title: In silico design of influenza a virus artificial epitope-based T-cell antigens and the evaluation of their immunogenicity in mice

description: The polyepitope strategy is promising approach for successfully creating a broadly protective flu vaccine, which targets T-lymphocytes (both CD4+ and CD8+) to recognise the most conserved epitopes of viral proteins. In this study, we employed a computer-aided approach to develop several artificial antigens potentially capable of evoking immune responses to different virus subtypes. These antigens included conservative T-cell epitopes of different influenza A virus proteins. To design epitope-based antigens we used experimentally verified information regarding influenza virus T-cell epitopes from the Immune Epitope Database (IEDB) (http://www.iedb.org). We constructed two “human” and two “murine” variants of polyepitope antigens. Amino acid sequences of target polyepitope antigens were designed using our original TEpredict/PolyCTLDesigner software. Immunogenic and protective features of DNA constructs encoding “murine” target T-cell immunogens were studied in BALB/c mice. We showed that mice groups immunised with a combination of computer-generated “murine” DNA immunogens had a 37.5% survival rate after receiving a lethal dose of either A/California/4/2009 (H1N1) virus or A/Aichi/2/68 (H3N2) virus, while immunisation with live flu H1N1 and H3N2 vaccine strains provided protection against homologous viruses and failed to protect against heterologous viruses. These results demonstrate that mechanisms of cross-protective immunity may be associated with the stimulation of specific T-cell responses. This study demonstrates that our computer-aided approach may be successfully used for rational designing artificial polyepitope antigens capable of inducing virus-specific T-lymphocyte responses and providing partial protection against two different influenza virus subtypes. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.13273103.v1
title: In silico design of influenza a virus artificial epitope-based T-cell antigens and the evaluation of their immunogenicity in mice

description: The polyepitope strategy is promising approach for successfully creating a broadly protective flu vaccine, which targets T-lymphocytes (both CD4+ and CD8+) to recognise the most conserved epitopes of viral proteins. In this study, we employed a computer-aided approach to develop several artificial antigens potentially capable of evoking immune responses to different virus subtypes. These antigens included conservative T-cell epitopes of different influenza A virus proteins. To design epitope-based antigens we used experimentally verified information regarding influenza virus T-cell epitopes from the Immune Epitope Database (IEDB) (http://www.iedb.org). We constructed two “human” and two “murine” variants of polyepitope antigens. Amino acid sequences of target polyepitope antigens were designed using our original TEpredict/PolyCTLDesigner software. Immunogenic and protective features of DNA constructs encoding “murine” target T-cell immunogens were studied in BALB/c mice. We showed that mice groups immunised with a combination of computer-generated “murine” DNA immunogens had a 37.5% survival rate after receiving a lethal dose of either A/California/4/2009 (H1N1) virus or A/Aichi/2/68 (H3N2) virus, while immunisation with live flu H1N1 and H3N2 vaccine strains provided protection against homologous viruses and failed to protect against heterologous viruses. These results demonstrate that mechanisms of cross-protective immunity may be associated with the stimulation of specific T-cell responses. This study demonstrates that our computer-aided approach may be successfully used for rational designing artificial polyepitope antigens capable of inducing virus-specific T-lymphocyte responses and providing partial protection against two different influenza virus subtypes. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.13227864
title: Integrated computational approach toward discovery of multi-targeted natural products from Thumbai (<i>Leucas aspera</i>) for attuning NKT cells

description: A multi-omics-based approach targeting the plant-based natural products from Thumbai (<i>Leucas aspera</i>), an important yet untapped potential source of many therapeutic agents for myriads of immunological conditions and genetic disorders, was conceptualized to reconnoiter its potential biomedical application. A library of 79 compounds from this plant was created, out of which 9 compounds qualified the pharmacokinetics parameters. Reverse pharmacophore technique for target fishing of the screened compounds was executed through which renin receptor (ATP6AP2) and thymidylate kinase (DTYMK) were identified as potential targets. Network biology approaches were used to comprehend and validate the functional, biochemical and clinical relevance of the targets. The target–ligand interaction and subsequent stability parameters at molecular scale were investigated using multiple strategies including molecular modeling, pharmacophore approaches and molecular dynamics simulation. Herein, isololiolide and 4-hydroxy-2-methoxycinnamaldehyde were substantiated as the lead molecules exhibiting comparatively the best binding affinity against the two putative protein targets. These natural lead products from <i>L. aspera</i> and the combinatorial effects may have plausible medical applications in a wide variety of neurodegenerative, genetic and developmental disorders. The lead molecules also exhibit promising alternative in diagnostics and therapeutics through immuno-modulation targeting natural killer T-cell function in transplantation-related pathogenesis, autoimmune and other immunological disorders. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.13227864.v1
title: Integrated computational approach toward discovery of multi-targeted natural products from Thumbai (<i>Leucas aspera</i>) for attuning NKT cells

description: A multi-omics-based approach targeting the plant-based natural products from Thumbai (<i>Leucas aspera</i>), an important yet untapped potential source of many therapeutic agents for myriads of immunological conditions and genetic disorders, was conceptualized to reconnoiter its potential biomedical application. A library of 79 compounds from this plant was created, out of which 9 compounds qualified the pharmacokinetics parameters. Reverse pharmacophore technique for target fishing of the screened compounds was executed through which renin receptor (ATP6AP2) and thymidylate kinase (DTYMK) were identified as potential targets. Network biology approaches were used to comprehend and validate the functional, biochemical and clinical relevance of the targets. The target–ligand interaction and subsequent stability parameters at molecular scale were investigated using multiple strategies including molecular modeling, pharmacophore approaches and molecular dynamics simulation. Herein, isololiolide and 4-hydroxy-2-methoxycinnamaldehyde were substantiated as the lead molecules exhibiting comparatively the best binding affinity against the two putative protein targets. These natural lead products from <i>L. aspera</i> and the combinatorial effects may have plausible medical applications in a wide variety of neurodegenerative, genetic and developmental disorders. The lead molecules also exhibit promising alternative in diagnostics and therapeutics through immuno-modulation targeting natural killer T-cell function in transplantation-related pathogenesis, autoimmune and other immunological disorders. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.13233903
title: Molecular dynamic study on PTEN frameshift mutations in breast cancer provide c2 domain as a potential biomarker

description: PTEN is a tumour suppressor gene known for regulating apoptosis, cell growth, and many other pathways. It is one of the most frequently mutated genes comprising the phosphatase domain (PD) and C terminal domain (C2). Direct therapeutic methods are not applicable for targeting PTEN because once gets mutated, it needs restoration. For mutant detection and restoration using PTEN mRNA there is a need to explore various mutations taking place in PTEN, identify their particular domains, and study their interactions within the cellular system. Here, we have tried to highlight a few such regions in the mutated PTEN of breast cancer patients. In this study, we have selected the top-most-occurring PTEN mutation in breast cancer and compared them to determine the specific properties of each mutation and its effect on functionality. Molecular dynamic simulation for 50 ns was performed on five structures to compare the structural behaviour of mutated PTEN in the system. Our finding suggests that frameshift mutations are more damaging and affect the c2 domain. Frameshift mutant fs_ACTT is the highest occurring as well as the most damaging mutation in all the compared structures. Docking study shows that substitution mutations D92H and R130Q causes loss of binding ability towards PIP2 in normal PTEN, interfering the dephosphorylation process. Overall, the C2 domain is more frequently mutated, and the amino acid residues in the C2 domain show more fluctuations compared to the other regions. Our study can provide the basis for selecting frequently mutated C2 domain as a potential therapeutic marker. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.13233903.v1
title: Molecular dynamic study on PTEN frameshift mutations in breast cancer provide c2 domain as a potential biomarker

description: PTEN is a tumour suppressor gene known for regulating apoptosis, cell growth, and many other pathways. It is one of the most frequently mutated genes comprising the phosphatase domain (PD) and C terminal domain (C2). Direct therapeutic methods are not applicable for targeting PTEN because once gets mutated, it needs restoration. For mutant detection and restoration using PTEN mRNA there is a need to explore various mutations taking place in PTEN, identify their particular domains, and study their interactions within the cellular system. Here, we have tried to highlight a few such regions in the mutated PTEN of breast cancer patients. In this study, we have selected the top-most-occurring PTEN mutation in breast cancer and compared them to determine the specific properties of each mutation and its effect on functionality. Molecular dynamic simulation for 50 ns was performed on five structures to compare the structural behaviour of mutated PTEN in the system. Our finding suggests that frameshift mutations are more damaging and affect the c2 domain. Frameshift mutant fs_ACTT is the highest occurring as well as the most damaging mutation in all the compared structures. Docking study shows that substitution mutations D92H and R130Q causes loss of binding ability towards PIP2 in normal PTEN, interfering the dephosphorylation process. Overall, the C2 domain is more frequently mutated, and the amino acid residues in the C2 domain show more fluctuations compared to the other regions. Our study can provide the basis for selecting frequently mutated C2 domain as a potential therapeutic marker. Communicated by Ramaswamy H. Sarma
DOI: 10.5519/qd.kn24jkjc
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (1001 records)
DOI: 10.3886/e127421v1-113320
title: Data and Code for: Subsidizing Fuel-Efficient Cars: Evidence from China's Automobile Industry

description: This paper examines the response of vehicle purchase behavior to China's largest national subsidy program for fuel-efficient vehicles during 2010 and 2011. Using variation from the program's eligibility cutoffs and the rollout of the subsidy program, the program is found to boost sales for subsidized vehicle models, but also to create a substitution effect within highly fuel-efficient vehicles. Estimates imply that ignoring the substitution effect would lead one to conclude that the program is welfare enhancing, whereas in fact the marginal cost of the program exceeds the marginal benefit by as much as 300 percent.
DOI: 10.34740/kaggle/ds/2027346
title: Chest Segmentation Image
DOI: 10.21227/1aqk-m533
title: Final Converted VTOL-UAV UX-7V Data

description: Flight data recorded during experiment.
DOI: 10.14469/hpc/10262
title: p-F-Ph-BF3 (-) 0.0 Cs d-aug-cc-pvdz

description: Gaussian 16 (C01) calculation
DOI: 10.14469/hpc/10263
title: p-F-Ph-BF3 (-) 90.0 Cs d-aug-cc-pvdz

description: Gaussian 16 (C01) calculation
DOI: 10.14469/hpc/10264
title: CFCl3 DMSO d-aug-cc-pvdz

description: Gaussian 16 (C01) calculation
DOI: 10.14469/hpc/10265
title: p-F-Ph-BF3 (-) 90.0 Cs aug-cc-pvdz

description: Gaussian 16 (C01) calculation
DOI: 10.14469/hpc/10266
title: p-F-Ph-BF3 (-) 0.0 Cs aug-cc-pvdz

description: Gaussian 16 (C01) calculation
DOI: 10.14469/hpc/10268
title: C2B2 Triplet G = -125.556678

description: Gaussian 16 (C01) calculation
DOI: 10.14469/hpc/10269
title: C2B2 singlet lowest G = -125.494653

description: Gaussian 16 (C01) calculation
DOI: 10.14469/hpc/10270
title: C2B2 singlet G = -125.484305

description: Gaussian 16 (C01) calculation
DOI: 10.14469/hpc/10273
title: 97, diaxial, d-aug-cc-pvdz on F, aug-cc-pvdz on Si

description: Gaussian 16 (C01) calculation
DOI: 10.14469/hpc/10274
title: PhBF2---thf syn G = -688.470846

description: Gaussian 16 (C01) calculation
DOI: 10.6084/m9.figshare.19402178.v1
title: extended data

description: This data contains :-1.Case Performa and Questionnaire2.inforned consent form3.Ethical approval letter
DOI: 10.14469/hpc/10279
title: UYELAN, 19F -56.4 19F expt Benzene -58.8 calc

description: Gaussian 16 (C01) calculation
DOI: 10.6084/m9.figshare.19401587.v1
title: Repository data

description: This data contains COSORT flow chart and Check List with reference to Article page number.
DOI: 10.6084/m9.figshare.19402178
title: extended data

description: This data contains :-1.Case Performa and Questionnaire2.inforned consent form3.Ethical approval letter
DOI: 10.6084/m9.figshare.19402178.v2
title: extended data

description: This data contains :-1.Case Performa and Questionnaire2.inforned consent form3.Ethical approval letter
DOI: 10.6084/m9.figshare.19425281
title: IJPR.dta

description: The data that support the findings of IJPR paper.
DOI: 10.6084/m9.figshare.19425281.v1
title: IJPR.dta

description: The data that support the findings of IJPR paper.
DOI: 10.25919/s0y8-3f45
title: Parkes observations for project P1101 semester 2021OCTS_17

description: We propose to carry out fortnightly monitoring of a very active repeater, FRB~190520, with the Parkes UWL system. Our current observations show that FRB~190520 is not only the most active FRB that can be observed with Parkes, but also shows unique behaviour at 2 to 3 GHz frequency. This makes UWL the ideal instrument to carry out in-depth studies of this repeating FRB. With this program, we expect to detect a large sample of bursts from FRB~190520, and in collaboration with the FAST telescope we will study emission properties, fluence distributions and polarisation properties over an extremely wide bandwidth with high sensitivity.
DOI: 10.6084/m9.figshare.19375664
title: Salsabil data

description: Data of diabetic type Sudanese patient<br>
DOI: 10.6084/m9.figshare.19375664.v1
title: Salsabil data

description: Data of diabetic type Sudanese patient<br>
DOI: 10.34740/kaggle/dsv/3361376
title: AutoXGB
DOI: 10.5281/zenodo.6384813
title: Datasets for "Comparison of multivariate ANOVA-based approaches for the determination of relevant variables in experimentally designed metabolomic studies"

description: <em><strong>Raw files of the LC-MS designed experiments.</strong></em> * <strong>YEAST GROWTH DATASET</strong> <strong>A) Phospholipids extraction</strong> - FosfoB1.raw - FosfoB3.raw - FosfoC2.raw - FosfoD1.raw - FosfoE1.raw - FosfoE2.raw - FosfoE3.raw <strong>B) Sphingolipids extraction</strong> - EsfingoB1.raw - EsfingoB2.raw - EsfingoC1.raw - EsfingoC2.raw - EsfingoC3.raw - EsfingoD1.raw - EsfingoD2.raw - EsfingoD3.raw <strong>* ZEBRAFISH DATASET</strong> <strong>A) BPA study</strong> Low BPA exposure - Low_BPA_A.d - Low_BPA_B.d - Low_BPA_C.d High_BPA_exposure - High_BPA_A.d - High_BPA_B.d - High_BPA_C.d Controls - Control_BPA_A.d -Control_BPA_B.d - Control_BPA_C.d <strong>B) Estradiol study</strong> Low E2 exposure - Low_E2_A.d - Low_E2_B.d - Low_E2_C.d High_E2_exposure - High_E2_A.d - High_E2_B.d - High_E2_C.d Controls - Control_E2_A.d -Control_E2_B.d - Control_E2_C.d <strong>Funding:</strong> This research was funded by the Spanish Ministry of Science and Innovation (MCI, Grant CTQ2017-82598-P) and Severo Ochoa Project CEX2018-000794-S (funded by MCIN/AEI/ 10.13039/501100011033), and supported from the Catalan Agency for Management of University and Research Grants (AGAUR, Grant 2017SGR753). MPC was funded by a predoctoral FPU 16/02640 scholarship from the Spanish Ministry of Education and Vocational Training (MEFP). The 1290 LC system and 6545 XT QTOF instrumentation were provided to DS as gifts by Agilent Technologies through their Thought Leader program.
DOI: 10.34740/kaggle/dsv/3361372
title: LUFlow Network Intrusion Detection Data Set
DOI: 10.5281/zenodo.6384812
title: Datasets for "Comparison of multivariate ANOVA-based approaches for the determination of relevant variables in experimentally designed metabolomic studies"

description: <em><strong>Raw files of the LC-MS designed experiments.</strong></em> * <strong>YEAST GROWTH DATASET</strong> <strong>A) Phospholipids extraction</strong> - FosfoB1.raw - FosfoB3.raw - FosfoC2.raw - FosfoD1.raw - FosfoE1.raw - FosfoE2.raw - FosfoE3.raw <strong>B) Sphingolipids extraction</strong> - EsfingoB1.raw - EsfingoB2.raw - EsfingoC1.raw - EsfingoC2.raw - EsfingoC3.raw - EsfingoD1.raw - EsfingoD2.raw - EsfingoD3.raw <strong>* ZEBRAFISH DATASET</strong> <strong>A) BPA study</strong> Low BPA exposure - Low_BPA_A.d - Low_BPA_B.d - Low_BPA_C.d High_BPA_exposure - High_BPA_A.d - High_BPA_B.d - High_BPA_C.d Controls - Control_BPA_A.d -Control_BPA_B.d - Control_BPA_C.d <strong>B) Estradiol study</strong> Low E2 exposure - Low_E2_A.d - Low_E2_B.d - Low_E2_C.d High_E2_exposure - High_E2_A.d - High_E2_B.d - High_E2_C.d Controls - Control_E2_A.d -Control_E2_B.d - Control_E2_C.d <strong>Funding:</strong> This research was funded by the Spanish Ministry of Science and Innovation (MCI, Grant CTQ2017-82598-P) and Severo Ochoa Project CEX2018-000794-S (funded by MCIN/AEI/ 10.13039/501100011033), and supported from the Catalan Agency for Management of University and Research Grants (AGAUR, Grant 2017SGR753). MPC was funded by a predoctoral FPU 16/02640 scholarship from the Spanish Ministry of Education and Vocational Training (MEFP). The 1290 LC system and 6545 XT QTOF instrumentation were provided to DS as gifts by Agilent Technologies through their Thought Leader program.
DOI: 10.5281/zenodo.6033766
title: The lysosome origin of biosilica machinery in the Demospongiae model Petrosia ficiformis (Poiret, 1789).

description: Proteomic LC-MS data for paper "The lysosome origin of biosilica machinery in the Demospongiae model Petrosia ficiformis (Poiret, 1789)."
DOI: 10.5281/zenodo.6033765
title: The lysosome origin of biosilica machinery in the Demospongiae model Petrosia ficiformis (Poiret, 1789).

description: Proteomic LC-MS data for paper "The lysosome origin of biosilica machinery in the Demospongiae model Petrosia ficiformis (Poiret, 1789)."
DOI: 10.5517/ccdc.csd.cc23p1sn
title: CCDC 1956651: Experimental Crystal Structure Determination

description: Related Article: Hao Li, Yu Tang, Kai-Yuan Liang, Yi Zang, Ezzat E.A. Osman, Ze-Xin Jin, Jia Li, Juan Xiong, Junmin Li, Jin-Feng Hu|2022|Phytochemistry|198|113161|doi:10.1016/j.phytochem.2022.113161