cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.13606548
title: Rational design of PIN1 inhibitors for cancer treatment based on conformational diversity analysis and docking based virtual screening

description: The parvulin PIN1 (peptidyl-prolyl cis-trans isomerase NIMA-interacting 1), is the only enzyme capable of isomerizing prolines of phospho-Serine/Threonine-Proline motifs. PIN1 binds to a subset of proteins and plays an essential role in regulating protein function post-phosphorylation control. Furthermore, the activity of PIN1 regulates the outcome of the signalling of proline-directed kinases (e.g. MAPK, CDK, or GSK3) and thus regulates cell proliferation and cell survival. For these reasons, PIN1 inhibitors are interesting since they may have therapeutic implications for cancer. Several authors have already reported that the non-structural point mutation Trp34Ala prevents PIN1 from interacting with its downstream effector proteins. In this work, we characterized PIN1 structurally, intending to explore new inhibition targets for the rational design of pharmacological activity compounds. Through a conformational diversity analysis of PIN1, we identified and characterized a highly specific druggable pocket around the residue Trp34. This pocket was used in a high-throughput docking screening of 450,000 drug-like compounds, and the top 10 were selected for re-docking studies on the previously used conformers. Finally, we evaluated the binding of each compound by thermal shift assay and found four molecules with a high affinity for PIN1 and potential inhibitory activity. Through this strategy, we achieved novel drug candidates with the ability to interfere with the phosphorylation-dependent actions of PIN1 and with potential applications in the treatment of cancer. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.13621775
title: Promising inhibitors of nsp2 of CHIKV using molecular docking and temperature-dependent molecular dynamics simulations

description: Infection due to the Chikungunya virus (CHIKV) has taken the life of lots of people; and researchers are working to find the vaccine or promisng drug candidates against this viral infection. In this work, the authors have designed one component reaction based on the thia-/oxa-azolidineone and created a library of 2000 molecules based on the product obtained. Further, the compounds were screened through the docking using iGemdock against the non-structural protein 2 (nsp2) of CHIKV. Molecular docking gives the binding energy (BE) or energy for the formation of the complex between the designed compound and nsp2 of CHIKV; and CMPD222 gave the lowest energy. This is based on the energy obtained from van der Waal’s interaction, hydrogen bonding and electrostatic instructions. Further, molecular dynamics simulations (MDS) of nsp2 of CHIKV with and without screened compound (222) were performed to validate the docking results and the change in free energy for the formation of the complex is −10.8327 kcal/mol. To explore the potential of CMPD222, the MDS of the CMPD222-nsp2 of CHIKV were performed at different temperatures (325, 350, 375 and 400 K) to understand the inhibition of the protease. MM-GBSA calculations were performed to determined change in entropy, change in enthalpy and change in free energy to understand the inhibition. Maximum inhibition of nsp2 of CHIKV with CMPD222 is observed at 375 K with a change in free energy of −19.3754 kcal/mol. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.13637312.v1
title: Physicochemical characterization of paclitaxel prodrugs with cytochrome 3A4 to correlate solubility and bioavailability implementing molecular docking and simulation studies

description: Prodrugs are biologically inactive drug molecules that may be developed through rational drug design with an objective to improve a drug’s pharmaceutical and pharmacokinetic properties. Paclitaxel, a highly potent anticancer drug, is directed against many cancers like breast cancer, ovarian cancer, lung cancer, head and neck tumors, non-small cell lung cancer, and Kaposi’s sarcoma, etc. Along with its excellent antitumor activity the drug had a major limitation of low water solubility. To overcome this limitation of this nanomolar active drug many prodrugs were formed in the past. Though increase in the solubility of the drug was obtained but that may or may not account for its increase in bioavailability. CYP3A4 liver enzymes are responsible for the metabolism of fifty percent of the drugs and are major metabolizing enzyme for paclitaxel. Phosphate prodrugs are well known to account the insolubility of many drugs and thus increasing their bioavailability also. In this study, we calculated the ADMET properties of a dataset of twenty phosphate prodrugs of paclitaxel. On the basis of reflection of three favourable properties, ten prodrugs were chosen for further docking studies against CYP3A4. Finally, three prodrugs showing unfavourable binding affinities were selected for Molecular Dynamics Simulations and from this <i>in-silico</i> study we identified that all the three selected prodrugs were unstable as compared to the paclitaxel. The instability of these prodrugs showed their lesser interaction with the CYP3A4 and hence contributing more towards its bioavailability. Thus the three suggested prodrugs those were studied <i>in-silico</i> for oral bioavailability can be further validated for gastrointestinal cancer. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.13606548.v1
title: Rational design of PIN1 inhibitors for cancer treatment based on conformational diversity analysis and docking based virtual screening

description: The parvulin PIN1 (peptidyl-prolyl cis-trans isomerase NIMA-interacting 1), is the only enzyme capable of isomerizing prolines of phospho-Serine/Threonine-Proline motifs. PIN1 binds to a subset of proteins and plays an essential role in regulating protein function post-phosphorylation control. Furthermore, the activity of PIN1 regulates the outcome of the signalling of proline-directed kinases (e.g. MAPK, CDK, or GSK3) and thus regulates cell proliferation and cell survival. For these reasons, PIN1 inhibitors are interesting since they may have therapeutic implications for cancer. Several authors have already reported that the non-structural point mutation Trp34Ala prevents PIN1 from interacting with its downstream effector proteins. In this work, we characterized PIN1 structurally, intending to explore new inhibition targets for the rational design of pharmacological activity compounds. Through a conformational diversity analysis of PIN1, we identified and characterized a highly specific druggable pocket around the residue Trp34. This pocket was used in a high-throughput docking screening of 450,000 drug-like compounds, and the top 10 were selected for re-docking studies on the previously used conformers. Finally, we evaluated the binding of each compound by thermal shift assay and found four molecules with a high affinity for PIN1 and potential inhibitory activity. Through this strategy, we achieved novel drug candidates with the ability to interfere with the phosphorylation-dependent actions of PIN1 and with potential applications in the treatment of cancer. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.13701252
title: Marine phycocompound screening reveals a potential source of novel senotherapeutics

description: Cells undergo a controlled and systematic cycle of growth, replication and death. However, the integrity of this process gradually declines, leading to accumulation of senescent cells, a major hallmark of biological ageing. Dietary algae, particularly marine algae, have been long reported to exert anti-ageing benefits as cosmeceuticals and nutraceuticals with limited understanding of the molecular mechanisms underlying their activity. In this study, we have incorporated 1,202 previously reported bioactive small phycocompounds and subjected them to cheminformatic queries to assess these interactions. <i>In-silico</i> ADMET, 2-phase docking, metabolic pathway interaction and molecular dynamics simulations reveal multiple marine phycocompounds to have safe and effective senolytic potentials. We employed a novel deep convolutional neural network driven screening approach to identify (2R*, 3S*, 6R*, 7S*, 10R*, 13R*)-7,13-Dihydroxy-2,6-cyclo-1(9),14-xenicadiene-18,19-dial derived from <i>Dilophus Fasciola</i>, Laurendecumenyne A from <i>Laurencia decumbens</i> and 4-Bromo-3-ethyl-9-[(2E)-2-penten-4-yn-1-yl]-2,8-dioxabicyclo[5.2.1]decan-6-ol from <i>Laurencia sp.</i> to be potent inhibitors of multiple target senescent-cell anti-apoptotic pathway proteins. We simulated the best overall target inhibitors, specific protein inhibitors and molecular pathway regulators with each target protein and found stable interactions with minimum deviations (mean RMSD = 0.17 ± 0.01 nm) and gyrations (mean Rg = 1.64 ± 0.16 nm) of the simulated protein-compound complexes. Finally, molecular mechanics calculation suggests potent (mean ΔG = −69.56 ± 27.19 kCal/mol) and frequent hydrophobic interactions between the top performing marine phycocompounds and target proteins. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.13701252.v1
title: Marine phycocompound screening reveals a potential source of novel senotherapeutics

description: Cells undergo a controlled and systematic cycle of growth, replication and death. However, the integrity of this process gradually declines, leading to accumulation of senescent cells, a major hallmark of biological ageing. Dietary algae, particularly marine algae, have been long reported to exert anti-ageing benefits as cosmeceuticals and nutraceuticals with limited understanding of the molecular mechanisms underlying their activity. In this study, we have incorporated 1,202 previously reported bioactive small phycocompounds and subjected them to cheminformatic queries to assess these interactions. <i>In-silico</i> ADMET, 2-phase docking, metabolic pathway interaction and molecular dynamics simulations reveal multiple marine phycocompounds to have safe and effective senolytic potentials. We employed a novel deep convolutional neural network driven screening approach to identify (2R*, 3S*, 6R*, 7S*, 10R*, 13R*)-7,13-Dihydroxy-2,6-cyclo-1(9),14-xenicadiene-18,19-dial derived from <i>Dilophus Fasciola</i>, Laurendecumenyne A from <i>Laurencia decumbens</i> and 4-Bromo-3-ethyl-9-[(2E)-2-penten-4-yn-1-yl]-2,8-dioxabicyclo[5.2.1]decan-6-ol from <i>Laurencia sp.</i> to be potent inhibitors of multiple target senescent-cell anti-apoptotic pathway proteins. We simulated the best overall target inhibitors, specific protein inhibitors and molecular pathway regulators with each target protein and found stable interactions with minimum deviations (mean RMSD = 0.17 ± 0.01 nm) and gyrations (mean Rg = 1.64 ± 0.16 nm) of the simulated protein-compound complexes. Finally, molecular mechanics calculation suggests potent (mean ΔG = −69.56 ± 27.19 kCal/mol) and frequent hydrophobic interactions between the top performing marine phycocompounds and target proteins. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.20098925.v2
title: Astragalus membranaceus (Fisch.) Bunge var. mongholicus (Bunge) P.K. Hsiao

description: The gene expression was detected during six different fruit developmental stages in <em>A. membranaceus</em> (Fisch.) Bunge var. mongholicus (Bunge) P.K. Hsiao.
DOI: 10.6084/m9.figshare.20098925
title: Astragalus membranaceus (Fisch.) Bunge var. mongholicus (Bunge) P.K. Hsiao

description: The gene expression was detected during six different fruit developmental stages in <em>A. membranaceus</em> (Fisch.) Bunge var. mongholicus (Bunge) P.K. Hsiao.
DOI: 10.6084/m9.figshare.20098925.v1
title: Data information.txt

description: The gene expression was detected during six different fruit developmental stages in <em>A. membranaceus</em> (Fisch.) Bunge var. mongholicus (Bunge) P.K. Hsiao.
DOI: 10.48420/20298747
title: Proteomic analysis of archaeological ceramics from Tell Khaiber, southern Iraq

description: Supplementary tables for the chapter 'Proteomic analysis of archaeological ceramics from Tell Khaiber, southern Iraq', to be presented with the university of Manchester thesis 'Analysis of Proteins from Archaeological Artefacts, with a Focus on Ancient Human Diet'
DOI: 10.48420/20298747.v1
title: Proteomic analysis of archaeological ceramics from Tell Khaiber, southern Iraq

description: Supplementary tables for the chapter 'Proteomic analysis of archaeological ceramics from Tell Khaiber, southern Iraq', to be presented with the university of Manchester thesis 'Analysis of Proteins from Archaeological Artefacts, with a Focus on Ancient Human Diet'
DOI: 10.48420/20298801
title: Machine Learning ATR-FTIR Spectroscopy Data for the Screening of Collagen for ZooMS Analysis and mtDNA in Archaeological Bone

description: Supplementary Tables for the article 'Machine Learning ATR-FTIR Spectroscopy Data for the Screening of Collagen for ZooMS Analysis and mtDNA in Archaeological Bone' for presentation with the University of Manchester Thesis 'Analysis of Proteins from Archaeological Artefacts, with a Focus on Ancient Human Diet'
DOI: 10.48420/20298801.v1
title: Machine Learning ATR-FTIR Spectroscopy Data for the Screening of Collagen for ZooMS Analysis and mtDNA in Archaeological Bone

description: Supplementary Tables for the article 'Machine Learning ATR-FTIR Spectroscopy Data for the Screening of Collagen for ZooMS Analysis and mtDNA in Archaeological Bone' for presentation with the University of Manchester Thesis 'Analysis of Proteins from Archaeological Artefacts, with a Focus on Ancient Human Diet'
DOI: 10.48420/20298750
title: Trends in Deamidation across Archaeological Bones, Ceramics and Dental Calculus

description: Supplementary tables for the chapter 'Trends in Deamidation across Archaeological Bones, Ceramics and Dental Calculus', to be presented along with the University of Manchester thesis 'Analysis of Proteins from Archaeological Artefacts, with a Focus on Ancient Human Diet'
DOI: 10.48420/20298750.v1
title: Trends in Deamidation across Archaeological Bones, Ceramics and Dental Calculus

description: Supplementary tables for the chapter 'Trends in Deamidation across Archaeological Bones, Ceramics and Dental Calculus', to be presented along with the University of Manchester thesis 'Analysis of Proteins from Archaeological Artefacts, with a Focus on Ancient Human Diet'
DOI: 10.48420/20298741
title: A Novel Deep Eutectic Solvent-based Protein Extraction Method for Pottery Residues and Archaeological Implications

description: Supplementary data for the chapter 'A Novel Deep Eutectic Solvent-based Protein Extraction Method for Pottery Residues and Archaeological Implications' for submission with University of Manchester thesis 'Analysis of Proteins fro Archaeological Artefacts, with a Focus on Ancient Human Diet'
DOI: 10.48420/20298741.v1
title: A Novel Deep Eutectic Solvent-based Protein Extraction Method for Pottery Residues and Archaeological Implications

description: Supplementary data for the chapter 'A Novel Deep Eutectic Solvent-based Protein Extraction Method for Pottery Residues and Archaeological Implications' for submission with University of Manchester thesis 'Analysis of Proteins fro Archaeological Artefacts, with a Focus on Ancient Human Diet'
DOI: 10.5258/soton/d2301
title: Dataset for article: 'Fundamental thermal noise in antiresonant hollow-core fibers'

description: The dataset supports the article to be published in Physical Review A It consists of Uploaded Archive (ZIP) containing 21 data files that are purely numerical (.txt) which underpin the figures in the article.
DOI: 10.14459/2022mp1663853
title: Dynamics of initial C allocation after drought release in mature Norway spruce

description: Data set used for the publication in the journal Global Change Biology, entitled "Dynamics of initial C allocation after drought release in mature Norway spruce - Increased belowground allocation of current photoassimilates covers only half of the C used for fine-root growth".
DOI: 10.6084/m9.figshare.11944947
title: More than one million negative reviews from a Chinese e-commerce platform

description: The dataset is from a B2C e-commerce platform in China, with massive product negative reviews of four representative sectors including Computers, Phone&Accessories, Gifts&Flowers and Clothing.Here the negative reviews are defined as the reviews with scores 1. After the raw data was collected, deduplication, user anonymization & categorization and text classification was employed to process the raw data. The data contains fields of id for comment, anonymous id for user, review text, timestamp of the posting, negative reason label and user level.<br> <br> The dataset contains four JSON files, with each file titled by the corresponding sector name.In each JSON file, each line represents a record of a negative review from this sector, in which the filed ‘id’ is the unique code we created for reviews, the filed ‘userID’ is the unique code we created for users, the field ‘userLevel’ is the user’s level in the platform, the field ‘creationTime’ is the timestamp a review was posted, the filed ‘content’ is the review text in Chinese and the field ‘label’ represent why the consumers post the negative reviews, in which 0 for Logistic, 1 for Product function, 2 for Consumer Service and 3 for False Marketing. <br> The dataset comes from our paper: <br> Sun M, Zhao J. Behavioral Patterns beyond Posting Negative Reviews Online: An Empirical View. <em>Journal of Theoretical and Applied Electronic Commerce Research</em>. 2022; 17(3):949-983. https://doi.org/10.3390/jtaer17030049 <br> If it is helpful, please cite the paper. <br> This work was supported by NSFC (Grant No. 71871006).
DOI: 10.6084/m9.figshare.20342781
title: Bionic Fishes and Real Fishes

description: Reflection data of Bionic Fishes and Real Fishes
DOI: 10.6084/m9.figshare.20342781.v2
title: Bionic Fishes and Real Fishes

description: Reflection data of Bionic Fishes and Real Fishes
DOI: 10.6084/m9.figshare.20342781.v1
title: Bionic Fishes and Real Fishes.zip

description: Reflection data of Bionic Fishes and Real Fishes
DOI: 10.48428/adattar/sx8zs5
title: DaLiCo collection

description: This upload contains presentations and assignments for the DaLiCo Summer School 2022 event.
DOI: 10.5281/zenodo.6866116
title: Provenance of Software Projects hosted on GitLab.com

description: Provenance of Software Projects hosted on GitLab - Data set
DOI: 10.5281/zenodo.6860657
title: Provenance of Software Projects hosted on GitLab.com

description: Provenance of Software Projects hosted on GitLab - Data set
DOI: 10.25919/f00z-kb02
title: Parkes observations for project P1152 semester 2022APRS_09

description: A large population of millisecond pulsars (MSPs) is expected in the Galactic bulge and is supported, among others, by the existence of a spatially extended gamma-ray excess emission discovered in Fermi-LAT data towards the inner Galaxy. Discovering MSPs in the Galactic bulge, would be a major breakthrough with strong impact onto several fields. In Berteaud et al. [2021a, 2021b], we have designed a new method to select bulge MSP candidates among Chandra X-ray cataloged sources. We also analysed imaging data of the VLA and identified 5 potential bulge MSP candidates, detected both with Chandra and VLA. Here we propose to follow up these 5 sources with the UWL receiver system on Parkes, which has the unique potential of probe their MSP nature thanks to multi-band, deep, observations. With the requested time, for two high-priority candidates, we will be able identify any bulge MSP with a pulse period P &gt; 1 ms. Three targets at lower priority can be identified as bulge MSP if their period is larger than 4 ms. Our goal is to provide the first multi-wavelength diagnostics of bulge MSPs, gather information about the MSP/pulsar ratio among the bulge X-ray candidates, and, finally, unveil the nature of the mysterious Fermi-LAT excess.
DOI: 10.5517/ccdc.csd.cc28pdhw
title: CCDC 2105938: Experimental Crystal Structure Determination

description: Related Article: Koffi Sénam Etsè, Guillermo Zaragoza, Albert Demonceau|2022|Polyhedron|224|116013|doi:10.1016/j.poly.2022.116013
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.6084/m9.figshare.20342877
title: Socio-economic statistics data

description: Socio-economic statistics data for China's poverty assessment and analysis under the framework of the UN SDGs
DOI: 10.5281/zenodo.6866250
title: Observation of Conductance Quantization in InSb Nanowire Networks

description: This file contains electron transport data and code of the paper "Observation of Conductance Quantization in InSb Nanowire Networks" Nano Lett. 2017, 17, 6511-6515.
DOI: 10.5281/zenodo.4989951
title: Observation of Conductance Quantization in InSb Nanowire Networks

description: This file contains electron transport data and code of the paper "Observation of Conductance Quantization in InSb Nanowire Networks" Nano Lett. 2017, 17, 6511-6515.
DOI: 10.6084/m9.figshare.20177366
title: Supplementary Data and Metadata from Pathways to primate hip function

description: Supplementary data and relevant metadata are included.
DOI: 10.6084/m9.figshare.20177366.v1
title: Supplementary Data and Metadata from Pathways to primate hip function

description: Supplementary data and relevant metadata are included.
DOI: 10.6084/m9.figshare.20320094
title: Supplementary code from Pathways to primate hip function

description: Understanding how diverse locomotor repertoires evolved in anthropoid primates is key to reconstructing the clade's evolution. Locomotor behaviour is often inferred from proximal femur morphology, yet the relationship of femoral variation to locomotor diversity is poorly understood. Extant acrobatic primates have greater ranges of hip joint mobility—particularly abduction—than those using more stereotyped locomotion, but how bony morphologies of the femur and pelvis interact to produce different locomotor abilities is unknown. We conducted hypothesis-driven path analyses via regularized structural equation modelling (SEM) to determine which morphological traits are the strongest predictors of hip abduction in anthropoid primates. Seven femoral morphological traits and two hip abduction measures were obtained from 25 primate species, split into broad locomotor and taxonomic groups. Through variable selection and fit testing techniques, insignificant predictors were removed to create the most parsimonious final models. Some morphological predictors, such as femur shaft length and neck-shaft angle, were important across models. Different trait combinations best predicted hip abduction by locomotor or taxonomic group, demonstrating group-specific linkages among morphology, mobility and behaviour. Our study illustrates the strength of SEM for identifying biologically important relationships between morphology and performance, which will have future applications for palaeobiological and biomechanical studies.