cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.23996730
title: Exploring potential <i>Plasmodium</i> kinase inhibitors: a combined docking, MD and QSAR studies

description: Malaria is a disease caused mostly by <i>Plasmodium</i> falciparum, affects millions of people each year. The kinases are validated targets for malaria infection. In this study, we investigate for real and hypothetical compounds that can inhibit cyclic guanosine monophosphate (CGMP)-dependent protein kinase using molecular docking <i>via</i> combined similarity analysis, molecular dynamics simulations, quantitative structure activity relationship (QSAR). Using Tanimoto similarity scores, ∼8.4 million compounds were screened. Compounds that have at least 70% similarity are used in further analysis. These compounds are assessed by means of docking, MMBPSA, MMGBSA and ANI_LIE. Based on consensus of different free energy methods and docking we revealed two potential inhibitors that can be useful for treatment of malaria. Apart from screening of real compounds, we have also selected the 10 most plausible hypothetical compounds by performing QSAR. By QSAR proposed pharmacophores, we generated over 247 hypothetical compounds and among them 19 molecules with lower QSAR predicted IC50 values and high docking scores were selected for further analysis. We selected the top 10 inhibitor candidates and performed MD simulations for free energy calculations like the protocol applied for real compounds. According to the free energy calculations, we suggest 2 real (C<sub>34</sub>H<sub>29</sub>F<sub>5</sub>N<sub>8</sub>O<sub>4</sub>S and C<sub>30</sub>H<sub>27</sub>F<sub>2</sub>N<sub>7</sub>O<sub>2</sub>S<sub>2</sub>, PubChem IDs: 140564801 and 89035196, respectively) and 2 hypothetical (C<sub>23</sub>H<sub>27</sub>FN<sub>6</sub>O<sub>2</sub>S, MOL3 and C<sub>23</sub>H<sub>25</sub>FN<sub>6</sub>O<sub>2</sub>S, MOL4) compounds that can be effective inhibitors against the protein kinase of <i>Plasmodium</i> falciparum. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.23996730.v1
title: Exploring potential <i>Plasmodium</i> kinase inhibitors: a combined docking, MD and QSAR studies

description: Malaria is a disease caused mostly by <i>Plasmodium</i> falciparum, affects millions of people each year. The kinases are validated targets for malaria infection. In this study, we investigate for real and hypothetical compounds that can inhibit cyclic guanosine monophosphate (CGMP)-dependent protein kinase using molecular docking <i>via</i> combined similarity analysis, molecular dynamics simulations, quantitative structure activity relationship (QSAR). Using Tanimoto similarity scores, ∼8.4 million compounds were screened. Compounds that have at least 70% similarity are used in further analysis. These compounds are assessed by means of docking, MMBPSA, MMGBSA and ANI_LIE. Based on consensus of different free energy methods and docking we revealed two potential inhibitors that can be useful for treatment of malaria. Apart from screening of real compounds, we have also selected the 10 most plausible hypothetical compounds by performing QSAR. By QSAR proposed pharmacophores, we generated over 247 hypothetical compounds and among them 19 molecules with lower QSAR predicted IC50 values and high docking scores were selected for further analysis. We selected the top 10 inhibitor candidates and performed MD simulations for free energy calculations like the protocol applied for real compounds. According to the free energy calculations, we suggest 2 real (C<sub>34</sub>H<sub>29</sub>F<sub>5</sub>N<sub>8</sub>O<sub>4</sub>S and C<sub>30</sub>H<sub>27</sub>F<sub>2</sub>N<sub>7</sub>O<sub>2</sub>S<sub>2</sub>, PubChem IDs: 140564801 and 89035196, respectively) and 2 hypothetical (C<sub>23</sub>H<sub>27</sub>FN<sub>6</sub>O<sub>2</sub>S, MOL3 and C<sub>23</sub>H<sub>25</sub>FN<sub>6</sub>O<sub>2</sub>S, MOL4) compounds that can be effective inhibitors against the protein kinase of <i>Plasmodium</i> falciparum. Communicated by Ramaswamy H. Sarma
DOI: 10.48668/7zbibi/xmpakf
title: 1.QC_readme.pdf

description: :unav
DOI: 10.48668/7zbibi
title: 1. Quality Control

description: Figures of QC. Remarks: respective figures of QC (errors, GC content and filter) were compressed into .tar file.
DOI: 10.48668/7zbibi/7orj4u
title: GC.tar

description: :unav
DOI: 10.48668/7zbibi/m5zr4n
title: Filter.tar

description: :unav
DOI: 10.48668/7zbibi/u9eopw
title: Error.tar

description: :unav
DOI: 10.48668/7zbibi/zeezfb
title: data_table.xls

description: :unav
DOI: 10.6084/m9.figshare.24005375
title: Delineation of the CENP-LN sub-complex dissociation mechanism upon multisite phosphorylation during mitosis

description: Phosphorylation is the most prevalent form of regulation in cells, organizing virtually all cellular functions, including survival, motility, differentiation, proliferation, and metabolism. This regulatory function has been largely conserved from the primitive single-cell to the more complex multicellular organisms. More than a third of proteins in eukaryotes are phosphorylated, and essentially every class of protein undergoes regulation by phosphorylation. A decline in the cellular level of CENP-L and CENP-N (components of the constitutive centromere associated network) has earlier been reported and linked to cyclin-dependent kinase (CDK) phosphorylation upon transition into mitosis. Given the importance of posttranslational modifications in cell cycle regulation, mechanistic comprehension of the impact of phosphorylation on both proteins (CENP-L and CENP-N) is of high significance. Through the application of diverse computational analytical techniques, including atomistic molecular dynamics simulations, the mechanism of kinetochore mis-localization and dissociation of the CENP-LN sub-complex in mitosis was delineated. We showed that the phosphorylation of both components of the sub-complex induces global conformational destabilizing effects on the proteins, combined with changes in the electrostatic potential and increase in steric clashes around the protein-protein interaction interface. This, consistent with earlier experimental reports, suggest that the multisite phosphorylation of the CENP-LN sub-complex plays a crucial role in the regulation of cell division. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.24005375.v2
title: Delineation of the CENP-LN sub-complex dissociation mechanism upon multisite phosphorylation during mitosis

description: Phosphorylation is the most prevalent form of regulation in cells, organizing virtually all cellular functions, including survival, motility, differentiation, proliferation, and metabolism. This regulatory function has been largely conserved from the primitive single-cell to the more complex multicellular organisms. More than a third of proteins in eukaryotes are phosphorylated, and essentially every class of protein undergoes regulation by phosphorylation. A decline in the cellular level of CENP-L and CENP-N (components of the constitutive centromere associated network) has earlier been reported and linked to cyclin-dependent kinase (CDK) phosphorylation upon transition into mitosis. Given the importance of posttranslational modifications in cell cycle regulation, mechanistic comprehension of the impact of phosphorylation on both proteins (CENP-L and CENP-N) is of high significance. Through the application of diverse computational analytical techniques, including atomistic molecular dynamics simulations, the mechanism of kinetochore mis-localization and dissociation of the CENP-LN sub-complex in mitosis was delineated. We showed that the phosphorylation of both components of the sub-complex induces global conformational destabilizing effects on the proteins, combined with changes in the electrostatic potential and increase in steric clashes around the protein-protein interaction interface. This, consistent with earlier experimental reports, suggest that the multisite phosphorylation of the CENP-LN sub-complex plays a crucial role in the regulation of cell division. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.24013844
title: An in-silico approach to the potential modulatory effect of taurine on sclerostin (SOST) and its probable role during osteoporosis

description: The cysteine-knot containing negative regulator of the Wnt (Wingless-related integration site) signaling pathway, sclerostin (SOST) is an emerging therapeutic target for osteoporosis. Its inhibition is responsible for the promotion of osteoblastogenesis. In this study, taurine, an amino sulfonic acid was used to study its mechanism of action for the inhibition of the SOST protein. Molecular docking and dynamic studies were performed as a part of the study whereby, it was observed that taurine binds to a probable allosteric pocket which allows it to modulate the structure of the SOST protein affecting all of the loops – loops 1, loop 2, and loop 3 – as well as the cysteine residues forming the cysteine-knot. The study also identified a set of seven taurine analogues that have better pharmacological activity than their parent compound using screening techniques. The conclusions derived from the study support that taurine has a probable antagonistic effect on the SOST protein directly through the modulation of HNQS motif and loops 2 and 3 and indirectly through its influence on the cysteine residues - 134, 165 and 167 C. Based on the results, it can be assumed that the binding of taurine with SOST protein probably reduces its binding affinity to the LRP6 protein greatly, while also inhibiting the target protein from anchoring to LRP4. Furthermore, it was noted that probable additional binding with any small molecule inhibitor (SMI) at the active site (PNAIG motif), in the presence of an already allosterically bound taurine, of the SOST protein would result in a complete potential antagonism of the target protein. Additionally, the study also uncovers the possible role of the GKWWRPS motif in providing stability to the PNAIG motif for the purpose of binding with LRP6. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.24013844.v1
title: An in-silico approach to the potential modulatory effect of taurine on sclerostin (SOST) and its probable role during osteoporosis

description: The cysteine-knot containing negative regulator of the Wnt (Wingless-related integration site) signaling pathway, sclerostin (SOST) is an emerging therapeutic target for osteoporosis. Its inhibition is responsible for the promotion of osteoblastogenesis. In this study, taurine, an amino sulfonic acid was used to study its mechanism of action for the inhibition of the SOST protein. Molecular docking and dynamic studies were performed as a part of the study whereby, it was observed that taurine binds to a probable allosteric pocket which allows it to modulate the structure of the SOST protein affecting all of the loops – loops 1, loop 2, and loop 3 – as well as the cysteine residues forming the cysteine-knot. The study also identified a set of seven taurine analogues that have better pharmacological activity than their parent compound using screening techniques. The conclusions derived from the study support that taurine has a probable antagonistic effect on the SOST protein directly through the modulation of HNQS motif and loops 2 and 3 and indirectly through its influence on the cysteine residues - 134, 165 and 167 C. Based on the results, it can be assumed that the binding of taurine with SOST protein probably reduces its binding affinity to the LRP6 protein greatly, while also inhibiting the target protein from anchoring to LRP4. Furthermore, it was noted that probable additional binding with any small molecule inhibitor (SMI) at the active site (PNAIG motif), in the presence of an already allosterically bound taurine, of the SOST protein would result in a complete potential antagonism of the target protein. Additionally, the study also uncovers the possible role of the GKWWRPS motif in providing stability to the PNAIG motif for the purpose of binding with LRP6. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.24045681
title: A Novel spice-antioxidant-based nano-vehicle as a putative green alternative of synthetic AChE inhibitor drugs

description: The present treatment for Alzheimer’s disease (AD) involves well known synthetic acetylcholine esterase (AChE) inhibitor drugs which besides having short duration of action also have deleterious impact on human health. Therefore, there is a need for natural plant-based biomolecule(s) with potential AChE inhibition activity (ies). The aim of the work is to design a spice-based nano-vehicle as a novel green alternative of synthetic AD drugs by nanoencapsulating a solvent-less supercritical CO<sub>2</sub> extract of small cardamom seeds (SC<sub>E</sub>) having a synergistic consortium of five antioxidant molecules, using polyethylene glycol and emulsifiers, selected based on Absorption, Distribution, Metabolism, Excretion, and Toxicity (ADMET) analyses. Ellman’s assay and enzyme inhibition kinetics of the antioxidant molecules as well as the extract and its nanoliposomal formulation (SC<sub>E</sub>-NL) were performed, followed by rigorous molecular docking and dynamics studies using MM-PBSA and umbrella sampling. The antioxidants exhibited significant AChE inhibition <i>in vitro</i>, individually with 1, 8-cineole having the least IC<sub>50</sub> value of 65.53 ± 0.05 µg/mL. . Although SC<sub>E</sub>-NL had higher IC<sub>50</sub> value (575.67 ± 0.5 µg/mL) vis-à-vis that of rivastigmine (67.52 ± 0.02 µg/mL), it is safer for usage being ‘green’.The Lineweaver-Burk plots (V<sub>max</sub> ∼1.04 mM/min) revealed competitive mode(s) of inhibition of AChE with each of these antioxidants. Binding energy analyses suggested very good binding free energies and stable docking/binding complexes (between the antioxidants and AChE). This study has delivered a nanoliposomal vehicle of food antioxidants as a putative ‘green’ alternative of synthetic AChE inhibitor drugs. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.24045681.v1
title: A Novel spice-antioxidant-based nano-vehicle as a putative green alternative of synthetic AChE inhibitor drugs

description: The present treatment for Alzheimer’s disease (AD) involves well known synthetic acetylcholine esterase (AChE) inhibitor drugs which besides having short duration of action also have deleterious impact on human health. Therefore, there is a need for natural plant-based biomolecule(s) with potential AChE inhibition activity (ies). The aim of the work is to design a spice-based nano-vehicle as a novel green alternative of synthetic AD drugs by nanoencapsulating a solvent-less supercritical CO<sub>2</sub> extract of small cardamom seeds (SC<sub>E</sub>) having a synergistic consortium of five antioxidant molecules, using polyethylene glycol and emulsifiers, selected based on Absorption, Distribution, Metabolism, Excretion, and Toxicity (ADMET) analyses. Ellman’s assay and enzyme inhibition kinetics of the antioxidant molecules as well as the extract and its nanoliposomal formulation (SC<sub>E</sub>-NL) were performed, followed by rigorous molecular docking and dynamics studies using MM-PBSA and umbrella sampling. The antioxidants exhibited significant AChE inhibition <i>in vitro</i>, individually with 1, 8-cineole having the least IC<sub>50</sub> value of 65.53 ± 0.05 µg/mL. . Although SC<sub>E</sub>-NL had higher IC<sub>50</sub> value (575.67 ± 0.5 µg/mL) vis-à-vis that of rivastigmine (67.52 ± 0.02 µg/mL), it is safer for usage being ‘green’.The Lineweaver-Burk plots (V<sub>max</sub> ∼1.04 mM/min) revealed competitive mode(s) of inhibition of AChE with each of these antioxidants. Binding energy analyses suggested very good binding free energies and stable docking/binding complexes (between the antioxidants and AChE). This study has delivered a nanoliposomal vehicle of food antioxidants as a putative ‘green’ alternative of synthetic AChE inhibitor drugs. Communicated by Ramaswamy H. Sarma
DOI: 10.15468/dl.zq3uuv
title: Occurrence Download

description: A dataset containing 13976 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Spain",
 "TaxonKey is Crataegus monogyna Jacq.",
 "Year 1901-2024"
 ]
}

 The dataset includes 13976 records from 90 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004079-241007104925546/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.48668/jzkmpm/l1e218
title: Transcript_length.xls

description: :unav
DOI: 10.48668/jzkmpm/ozypbv
title: Unigene_bar.png

description: :unav
DOI: 10.48668/jzkmpm/zvyvzb
title: Unigene_length_distribution.png

description: :unav
DOI: 10.48668/jzkmpm/2qtilg
title: Trinity.assembly.stat.xls

description: :unav
DOI: 10.48668/jzkmpm/4b2wyl
title: Trinity.fasta

description: :unav
DOI: 10.48668/jzkmpm/mdkzcr
title: Transcript_bar.png

description: :unav
DOI: 10.48668/jzkmpm/usshpm
title: Trinity.sequence_length.stat.xls

description: :unav
DOI: 10.48668/jzkmpm/ya32rh
title: cluster_all.fasta

description: :unav
DOI: 10.48668/jzkmpm
title: 2. Assembly

description: Result of De novo assembly.
DOI: 10.48668/jzkmpm/923vj1
title: Unigene_Transcript.length_distribution.png

description: :unav
DOI: 10.48668/jzkmpm/aeuit0
title: 2.Assembly.README.pdf

description: :unav
DOI: 10.48668/jzkmpm/apjugc
title: Unigene_length.xls

description: :unav
DOI: 10.48668/jzkmpm/iwozpv
title: unigene.fasta

description: :unav
DOI: 10.48668/jzkmpm/r3wcrv
title: Transcript_length_distribution.png

description: :unav
DOI: 10.48668/nkdpfn/ro8ahz
title: None_unigene.blast.cds.fasta

description: :unav
DOI: 10.48668/nkdpfn/fznqhy
title: unigene.cds_prediction.summary.xls

description: :unav
DOI: 10.48668/nkdpfn/g1nq0d
title: Initiation_only_unigene.blast.cds.fasta

description: :unav
DOI: 10.48668/nkdpfn/mclghz
title: unigene.transdecoder.cds.png

description: :unav
DOI: 10.48668/nkdpfn/mmboqm
title: unigene.blast.pep.png

description: :unav
DOI: 10.48668/nkdpfn/tralzs
title: unigene.blast.cds.fasta

description: :unav
DOI: 10.48668/nkdpfn/xpmcsb
title: 4.CDSprediction_readme.pdf

description: :unav
DOI: 10.48668/nkdpfn
title: 4. CDS Prediction

description: Prediction of CDS genes
DOI: 10.48668/nkdpfn/5rdxya
title: Termination_only_unigene.blast.cds.fasta

description: :unav
DOI: 10.48668/nkdpfn/g25rfp
title: unigene.transdecoder.pep.png

description: :unav
DOI: 10.48668/nkdpfn/jkzegl
title: Both_unigene.blast.cds.fasta

description: :unav
DOI: 10.48668/nkdpfn/jtwv9d
title: unigene.blast.pep.fasta

description: :unav
DOI: 10.48668/nkdpfn/zilln5
title: unigene.blast.cds.png

description: :unav
DOI: 10.6084/m9.figshare.27193626
title: ERSP data

description: This CSV contains data for both the intervention group (vXX) and the control group (cXX). One participant has two sessions (before- and after-stimulation test sessions), each with 20 trials. "Pre" means the before-stimulation test session, and "pos" means the after-stimulation test session. The original ERSP values were four-dimensional, consisting of time, frequency, trials, and subjects. For the current dataset, the time points during the imagery phase were extracted, and the frequency bands were limited to the alpha and beta ranges. By taking the median values within these ranges, the data were reduced to two dimensions, representing trials and subjects.The missing data points indicate that certain trials were rejected due to issues such as poor EEG data quality.
DOI: 10.48668/ikt38n/bdmcpb
title: violin.pdf

description: :unav
DOI: 10.48668/ikt38n/ejpszu
title: mapping_rate.xls

description: :unav
DOI: 10.48668/ikt38n/vjkzkf
title: boxplot.pdf

description: :unav
DOI: 10.48668/ikt38n/26j1v8
title: FPKM_density_distribution-1716465706612.pdf

description: :unav
DOI: 10.48668/ikt38n/eaxm0f
title: interval.bar.pdf

description: :unav
DOI: 10.48668/ikt38n/h3uulx
title: readcount.xls

description: :unav
DOI: 10.48668/ikt38n/mthgvh
title: fpkm_interval.xls

description: :unav
DOI: 10.48668/ikt38n/nkbnhf
title: gene_fpkm.xls

description: :unav
DOI: 10.48668/ikt38n
title: 5. Quantification

description: Quantification of gene expression normalized in Fragments Per Kilobase of transcript per Million mapped reads (FPKM).
DOI: 10.48668/ikt38n/1swujg
title: PCA2D_group5.pdf

description: :unav
DOI: 10.48668/ikt38n/de7app
title: correlation.xls

description: :unav
DOI: 10.48668/ikt38n/vfy412
title: PCA2D_group4.pdf

description: :unav
DOI: 10.48668/ikt38n/vovpkc
title: PCA2D_group3.pdf

description: :unav
DOI: 10.48668/kaqtkr/jgugmn
title: unigene.fasta.ssr_motif_frequency.xls

description: :unav
DOI: 10.48668/kaqtkr/bhnbu0
title: unigene.SSR_primer.xls

description: :unav
DOI: 10.48668/kaqtkr/i6jd9o
title: unigene.SSR_position.xls

description: :unav
DOI: 10.48668/kaqtkr/sn1he2
title: unigene.fasta.ssr_classification.xls

description: :unav
DOI: 10.48668/kaqtkr/wfvypp
title: unigene.fasta.ssr_summary.xls

description: :unav
DOI: 10.48668/kaqtkr/xa8em2
title: unigene.fasta.SSR_motifs_distribution.png

description: :unav
DOI: 10.5281/zenodo.13907446
title: Zabö Integrated Farming System

description: This file includes the location boundary .shp file of the 3 GIAHS sites in India, AOI(Zabö) boundary .Shp file and the point location of the catchments.
DOI: 10.5281/zenodo.13907447
title: Zabö Integrated Farming System

description: This file includes the location boundary .shp file of the 3 GIAHS sites in India, AOI(Zabö) boundary .Shp file and the point location of the catchments.
DOI: 10.48668/kaqtkr
title: 8. Detection of SSR

description: Detection of Simple Sequence Repeats (SSR).
DOI: 10.48668/kaqtkr/kh5amm
title: unigene.fasta.repeat_type_frequency.xls

description: :unav
DOI: 10.48668/kaqtkr/nyj47r
title: 8.SSRdetection_readme.pdf

description: :unav
DOI: 10.48668/2fsr1j/csxoa9
title: 2.KEGG.tar

description: :unav
DOI: 10.48668/2fsr1j/tivscn
title: 3.PPI.tar

description: :unav
DOI: 10.48668/2fsr1j
title: 7. Functional Enrichment Analysis

description: Result of Functional Enrichment Analysis. Databases including Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were adopted to annotate genes with biological functions. GO, KEGG and PPI were compressed as .tar files.
DOI: 10.48668/2fsr1j/ibqjq6
title: 1.GO.tar

description: :unav
DOI: 10.48668/2fsr1j/tuiq32
title: 7.Enrichment_readme.pdf

description: :unav
DOI: 10.15468/dl.dapy2h
title: Occurrence Download

description: A dataset containing 37828 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Mosquito Alert Dataset"
 ]
}

 The dataset includes 37828 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004082-241007104925546/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.48668/wrwmzg
title: 9. Detection of SNP and InDels

description: Detection of Single Nucleotide Polymorphism (SNP) and Insertion-Deletions (InDels).
DOI: 10.48668/wrwmzg/03uypw
title: SNP_info.xls

description: :unav
DOI: 10.48668/wrwmzg/1ztzkq
title: 9.SNP_readme.pdf

description: :unav
DOI: 10.48668/wrwmzg/zucnwv
title: SNPs.xls

description: :unav
DOI: 10.48668/wrwmzg/hcqjr1
title: InDels.xls

description: :unav
DOI: 10.6084/m9.figshare.27194043.v1
title: HiFiBGC_0.1.13_Run.tar.gz

description: This dataset contains select files and folders from the output of HiFiBGC run on four HiFi metagenomic datasets. It is used for the analyses available here https://github.com/ay-amityadav/HiFiBGC_analyses.<br>
DOI: 10.15468/dl.ymrdmv
title: Occurrence Download

description: A dataset containing 29 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Alexteroon obstetricans (Ahl, 1931)"
 ]
}

 The dataset includes 29 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004086-241007104925546/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.