cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.24347356
title: Molecular dynamics investigations of human DNA-topoisomerase I interacting with novel Dewar Valence photo-adducts: insights into inhibitory activity (best poses)

description: Chronic exposure to ultraviolet (UV) radiation is known to induce the formation of both cyclobutane pyrimidine dimers (CPDs) and Dewar valence photo-adducts (DVs) in DNA. While CPDs occur at a frequency three or four times greater than DVs, recent studies have unveiled that the latter display superior selectivity and significant stability in interaction with the human DNA/Topoisomerase 1 complex, highlighting notable anti-melanoma properties. To better comprehend the behaviour of these thymine-based photoadduct ligands (DV) in a biological context, we conducted four all-atom molecular dynamic simulations spanning 1 microsecond. These simulations examined the stability and conformational changes of two DNA/TOP1-DV complexes in solution, and their molecular counterparts, DNA/TOP1-biomimetic thymine dimers. Results from root-mean-square deviation (RMSD) and root-mean-square fluctuation (RMSF) analyses unequivocally confirmed increased stability of the DNA/TOP1-DV complexes throughout the simulation duration. Furthermore, we performed detailed interaction analyses, uncovering the presence of salt bridges, hydrogen bonds, water-mediated interactions, hydrophobic interactions, and π stacking interactions. Ultimately, pinpointing the non-covalent interactions within the complexes enabled the evaluation of receptor residues involved in these interactions and proposed a potential TOP1 inhibition mechanism. These findings emphasise the prospective use of DV photo-adducts as antitumor agents. Our study may pave new avenues in cancer therapy.
DOI: 10.6084/m9.figshare.24347356.v1
title: Best poses

description: Chronic exposure to ultraviolet (UV) radiation is known to induce the formation of both cyclobutane pyrimidine dimers (CPDs) and Dewar valence photo-adducts (DVs) in DNA. While CPDs occur at a frequency three or four times greater than DVs, recent studies have unveiled that the latter display superior selectivity and significant stability in interaction with the human DNA/Topoisomerase 1 complex, highlighting notable anti-melanoma properties. To better comprehend the behaviour of these thymine-based photoadduct ligands (DV) in a biological context, we conducted four all-atom molecular dynamic simulations spanning 1 microsecond. These simulations examined the stability and conformational changes of two DNA/TOP1-DV complexes in solution, and their molecular counterparts, DNA/TOP1-biomimetic thymine dimers. Results from root-mean-square deviation (RMSD) and root-mean-square fluctuation (RMSF) analyses unequivocally confirmed increased stability of the DNA/TOP1-DV complexes throughout the simulation duration. Furthermore, we performed detailed interaction analyses, uncovering the presence of salt bridges, hydrogen bonds, water-mediated interactions, hydrophobic interactions, and π stacking interactions. Ultimately, pinpointing the non-covalent interactions within the complexes enabled the evaluation of receptor residues involved in these interactions and proposed a potential TOP1 inhibition mechanism. These findings emphasise the prospective use of DV photo-adducts as antitumor agents. Our study may pave new avenues in cancer therapy.
DOI: 10.5281/zenodo.10014403
title: 3x2pt Gaussian + SSC Covariance Matrix

description: 3x2pt Gaussian + SSC covariance matrix to be used as input to CLOE for the MCMC runsThe Gauss+SSC covariance matrix is provided both in ASCII (.dat) and binary (.npy) format 
For comparison, the Gauss only case is also uploaded
The covariance refers for the full data vector without any scale cuts so the total dimension is N x N with N = NoEll x [NoBinsWL (NoBinsWL + 1)/2 + NoBinsGC x NoBinsGC + NoBinsGC (NoBinsGC + 1)/2]with NoEll = number of multipoles = 32NoBinsWL = number of redshift bins for WL = 13NoBinsGC = number of redshift bins for GC = 13 thus giving N = 11232.
DOI: 10.5281/zenodo.8418723
title: 3x2pt Gaussian + SSC Covariance Matrix

description: 3x2pt Gaussian + SSC covariance matrix to be used as input to CLOE for the MCMC runsThe Gauss+SSC covariance matrix is provided both in ASCII (.dat) and binary (.npy) format 
For comparison, the Gauss only case is also uploaded
The covariance refers for the full data vector without any scale cuts so the total dimension is N x N with N = NoEll x [NoBinsWL (NoBinsWL + 1)/2 + NoBinsGC x NoBinsGC + NoBinsGC (NoBinsGC + 1)/2]with NoEll = number of multipoles = 32NoBinsWL = number of redshift bins for WL = 13NoBinsGC = number of redshift bins for GC = 13 thus giving N = 11232.
DOI: 10.5281/zenodo.8418724
title: 3x2pt Gaussian + SSC Covariance Matrix

description: 3x2pt Gaussian + SSC covariance matrix to be used as input to CLOE for the MCMC runs Matrices available in zipped ASCII (.dat.zip) and npy (.npy) format The file with the "-inv" is for the inverted matrix For comparison, the Gaussian only covariance matrix is stored too
DOI: 10.34740/kaggle/dsv/6741568
title: DanfeNER
DOI: 10.5281/zenodo.10022844
title: LiFE Benchmark files for CLOE validation

description: Gzipped tar archive containing all the files needed for CLOE validation against LiFE
DOI: 10.5281/zenodo.10022843
title: LiFE Benchmark files for CLOE validation

description: Gzipped tar archive containing all the files needed for CLOE validation against LiFE
DOI: 10.5281/zenodo.10022676
title: Genome and Transcriptome references based on hg19 from UCSC, 2015

description: rsem.transcripts.nant2015.fa.gz - bgzipped FASTA reference of transcriptomes
genome.nant2015.fa.gz - bgzipped FASTA human genome reference, with several viral sequences added.
refseq.txt.gz - Exact sequence accessions and mapping coordinates for a RefSeq transcriptome based off the UCSC genome browser for hg19.
Coordinates are BED-style, with one row per transcript, and 1+ transcript per gene.
Column annotation
1. RefSeq Accession
2. Chromosome
3. Strand
4. thinStart (gene boundary, including UTR)
5. thinEnd (gene boundary, including UTR)
6. thickStart (CDS boundary)
7. thinStart (CDS boundary)
8. number of exons
9. comma separated exon starts
10. comma separate exon ends
11. common gene name
12. refseq gene id
13. 0 if non-primary transcript, 1 if primary transcript
DOI: 10.5281/zenodo.8432436
title: Genome and Transcriptome references based on hg19 from UCSC, 2015

description: rsem.transcripts.nant2015.fa.gz - bgzipped FASTA reference of transcriptomes
genome.nant2015.fa.gz - bgzipped FASTA human genome reference, with several viral sequences added.
refseq.txt.gz - Exact sequence accessions and mapping coordinates for a RefSeq transcriptome based off the UCSC genome browser for hg19.
Coordinates are BED-style, with one row per transcript, and 1+ transcript per gene.
Column annotation
1. RefSeq Accession
2. Chromosome
3. Strand
4. thinStart (gene boundary, including UTR)
5. thinEnd (gene boundary, including UTR)
6. thickStart (CDS boundary)
7. thinStart (CDS boundary)
8. number of exons
9. comma separated exon starts
10. comma separate exon ends
11. common gene name
12. refseq gene id
13. 0 if non-primary transcript, 1 if primary transcript
DOI: 10.5281/zenodo.8432437
title: Transcriptome of RefSeq version downloaded from UCSC Genome Browser Dec 2015

description: Exact sequence accessions and mapping coordinates for a RefSeq transcriptome based off the UCSC genome browser for hg19. Coordinates are BED-style, with one row per transcript, and 1+ transcript per gene. Column annotation 1. RefSeq Accession 2. Chromosome 3. Strand 4. thinStart (gene boundary, including UTR) 5. thinEnd (gene boundary, including UTR) 6. thickStart (CDS boundary) 7. thinStart (CDS boundary) 8. number of exons 9. comma separated exon starts 10. comma separate exon ends 11. common gene name 12. refseq gene id 13. 0 if non-primary transcript, 1 if primary transcript
DOI: 10.34740/kaggle/ds/2210947
title: EverestNER
DOI: 10.5517/ccdc.csd.cc2c77rm
title: CCDC 2181710: Experimental Crystal Structure Determination

description: Related Article: Si-Meng Zhang, Yue Wang, Yuan-Yuan Ma, Zhao-Bin Li, Jing Du, Zhan-Gang Han|2022|Inorg.Chem.|61|20596|doi:10.1021/acs.inorgchem.2c03472
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: 10.5517/ccdc.csd.cc2c77sn
title: CCDC 2181711: Experimental Crystal Structure Determination

description: Related Article: Si-Meng Zhang, Yue Wang, Yuan-Yuan Ma, Zhao-Bin Li, Jing Du, Zhan-Gang Han|2022|Inorg.Chem.|61|20596|doi:10.1021/acs.inorgchem.2c03472
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: 10.5517/ccdc.csd.cc2cn8gs
title: CCDC 2194225: Experimental Crystal Structure Determination

description: Related Article: Shan-Shan Chen, Xiu-Ying Zheng, HaiQuan Tian, La-Sheng Long, Lan-Sun Zheng, Xiang-Jian Kong|2022|Inorg.Chem.|61|20365|doi:10.1021/acs.inorgchem.2c03007
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: 10.5517/ccdc.csd.cc2cn8ht
title: CCDC 2194226: Experimental Crystal Structure Determination

description: Related Article: Shan-Shan Chen, Xiu-Ying Zheng, HaiQuan Tian, La-Sheng Long, Lan-Sun Zheng, Xiang-Jian Kong|2022|Inorg.Chem.|61|20365|doi:10.1021/acs.inorgchem.2c03007
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: 10.5517/ccdc.csd.cc2djlp7
title: CCDC 2220489: Experimental Crystal Structure Determination

description: Related Article: Zhiwei Ma, Yuyuan Wang, Yanyan Liu, Gaoyu Li, Junliang Zhou, Juan Zhao, Zhiyong Yang, Zhenguo Chi|2023|Dyes Pigm.|215|111298|doi:10.1016/j.dyepig.2023.111298
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: 10.5517/ccdc.csd.cc2dn7x7
title: CCDC 2223999: Experimental Crystal Structure Determination

description: Related Article: Ashlie N. Walker, Megan A. Ayala, Somrita Mondal, Mackenzie C. Bergagnini, Phuong John D. Bui, Stephanie N. Chidester, Chad I. Doeden, Louise Esjornson, Brian R. Sweany, Leslie Garcia, Jeanette A. Krause, Allen G. Oliver, Timothy J. Prior, Timothy J. Hubin|2023|Molecules|28|895|doi:10.3390/molecules28020895
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: 10.5517/ccdc.csd.cc2d6p5h
title: CCDC 2210956: Experimental Crystal Structure Determination

description: Related Article: Guanping Li, Olaf Stefanczyk, Kunal Kumar, Yuuki Mineo, Koji Nakabayashi, Shin‐ichi Ohkoshi|2023|Angew.Chem.,Int.Ed.|62|e202214673|doi:10.1002/anie.202214673
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: 10.5517/ccdc.csd.cc2dn7y8
title: CCDC 2224000: Experimental Crystal Structure Determination

description: Related Article: Ashlie N. Walker, Megan A. Ayala, Somrita Mondal, Mackenzie C. Bergagnini, Phuong John D. Bui, Stephanie N. Chidester, Chad I. Doeden, Louise Esjornson, Brian R. Sweany, Leslie Garcia, Jeanette A. Krause, Allen G. Oliver, Timothy J. Prior, Timothy J. Hubin|2023|Molecules|28|895|doi:10.3390/molecules28020895
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: 10.6073/pasta/e02f855d69193a46571168575b35291d
title: Structural Diversity from the NEON Discrete-Return LiDAR Point Cloud in 2013-2022

description: Structural diversity, characterizing the volumetric capacity and physical arrangement of biotic components in an ecosystem, controls critical ecosystem functions like light interception, hydrology, and microclimate. This product generates structural diversity metrics for the NEON sites, sourced from the Discrete-Return LiDAR Point Cloud from the NEON Aerial Observation Platform (DP1.30003.001; collected in March 2023). Using R programming, we computed the metrics detailing height, heterogeneity, and density at 30 m, aligned to the Landsat grids, for 243 site years in 57 NEON sites from 2013 to 2022.
DOI: 10.6084/m9.figshare.23928468.v2
title: minus_assembly_dataset

description: Contains seven items:<i>V. vitis-idaea</i> ssp. <i>minus</i> <i>de novo</i> assembly in fasta format.<i>V. vitis-idaea</i> ssp. <i>minus</i> scaffolded assembly by mapping to the bilberry genome in agp format based on contig names in the <i>de novo</i> assembled genome (<i>V. myrtillus</i>; Wu et al. 2021).<i>V. vitis-idaea</i> ssp. <i>minus</i> scaffolded assembly by mapping to the bilberry genome in fasta format (<i>V. myrtillus</i>; Wu et al. 2021).Annotation of genes/mRNAs associated with the scaffolded genome in .gff3 format.Protein sequences from gene annotation in amino acid fasta or faa format.Coding sequences in nucleotide fasta format.Annotation of transposable elements associated with the scaffolded genome in gff3 format.Raw sequences generated in this study are found in NCBI under PRJNA998787: Oxford Nanopore (SRR25468432-SRR25468441), Illumina NovaSeq (SRR25477289)The contig-level assembly fasta can also be found in NCBI: JAUYVF000000000Reference: Wu,C., Deng,C., Hilario,E., Albert,N., Lafferty,D., Plunkett,B., Elborough,C., Saei,A., Jaakola,L., Karppinen,K., Grande,A., Kylli,R., Allan,A., Espley,R. and Chagne,D. 2021. A chromosome-scale assembly of the bilberry genome identifies a complex locus controlling berry anthocyanin composition. Molecular Ecology Resources, DOI 10.1111/1755-0998.13467
DOI: 10.6084/m9.figshare.23926251.v2
title: RedCandy_assembly_dataset

description: Contains seven items:<i>V. vitis-idaea</i> ssp. <i>vitis-idaea</i><i> </i>var. 'Red Candy' <i>de novo</i> assembly in fasta format.<i>V. vitis-idaea</i> ssp. <i>vitis-idaea</i><i> </i>var. 'Red Candy' scaffolded assembly by mapping to the bilberry genome in agp format based on contig names in the <i>de novo</i> assembled genome (<i>V. myrtillus</i>; Wu et al. 2021).<i>V. vitis-idaea</i> ssp. <i>vitis-idaea</i><i> </i>var. 'Red Candy' scaffolded assembly by mapping to the bilberry genome in fasta format (<i>V. myrtillus</i>; Wu et al. 2021).Annotation of genes/mRNAs associated with the scaffolded genome in gff3 format.Protein sequences from gene annotation in amino acid fasta or faa format.Coding sequences in nucleotide fasta format.Annotation of transposable elements associated with the scaffolded genome in gff3 format.Raw sequences generated in this study are found in NCBI under PRJNA998787: Oxford Nanopore (SRR25468442-SRR25468450), Illumina NovaSeq (SRR25477290)The contig-level assembly fasta can also be found in NCBI: JAUYVE000000000Reference: Wu,C., Deng,C., Hilario,E., Albert,N., Lafferty,D., Plunkett,B., Elborough,C., Saei,A., Jaakola,L., Karppinen,K., Grande,A., Kylli,R., Allan,A., Espley,R. and Chagne,D. 2021. A chromosome-scale assembly of the bilberry genome identifies a complex locus controlling berry anthocyanin composition. Molecular Ecology Resources, DOI 10.1111/1755-0998.13467
DOI: 10.5519/qd.2lw2dpiz
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (1 records)
DOI: 10.5281/zenodo.10018440
title: Reactome Data 86 - Neo4j & MySQL
DOI: 10.5281/zenodo.10018439
title: Reactome Data 86 - Neo4j & MySQL
DOI: 10.6084/m9.figshare.23926251
title: RedCandy_assembly_dataset

description: Contains seven items:<i>V. vitis-idaea</i> ssp. <i>vitis-idaea</i><i> </i>var. 'Red Candy' <i>de novo</i> assembly in fasta format.<i>V. vitis-idaea</i> ssp. <i>vitis-idaea</i><i> </i>var. 'Red Candy' scaffolded assembly by mapping to the bilberry genome in agp format based on contig names in the <i>de novo</i> assembled genome (<i>V. myrtillus</i>; Wu et al. 2021).<i>V. vitis-idaea</i> ssp. <i>vitis-idaea</i><i> </i>var. 'Red Candy' scaffolded assembly by mapping to the bilberry genome in fasta format (<i>V. myrtillus</i>; Wu et al. 2021).Annotation of genes/mRNAs associated with the scaffolded genome in gff3 format.Protein sequences from gene annotation in amino acid fasta or faa format.Coding sequences in nucleotide fasta format.Annotation of transposable elements associated with the scaffolded genome in gff3 format.Raw sequences generated in this study are found in NCBI under PRJNA998787: Oxford Nanopore (SRR25468442-SRR25468450), Illumina NovaSeq (SRR25477290)The contig-level assembly fasta can also be found in NCBI: JAUYVE000000000Reference: Wu,C., Deng,C., Hilario,E., Albert,N., Lafferty,D., Plunkett,B., Elborough,C., Saei,A., Jaakola,L., Karppinen,K., Grande,A., Kylli,R., Allan,A., Espley,R. and Chagne,D. 2021. A chromosome-scale assembly of the bilberry genome identifies a complex locus controlling berry anthocyanin composition. Molecular Ecology Resources, DOI 10.1111/1755-0998.13467
DOI: 10.6084/m9.figshare.23926251.v3
title: RedCandy_assembly_dataset

description: Contains seven items:<i>V. vitis-idaea</i> ssp. <i>vitis-idaea</i><i> </i>var. 'Red Candy' <i>de novo</i> assembly in fasta format.<i>V. vitis-idaea</i> ssp. <i>vitis-idaea</i><i> </i>var. 'Red Candy' scaffolded assembly by mapping to the bilberry genome in agp format based on contig names in the <i>de novo</i> assembled genome (<i>V. myrtillus</i>; Wu et al. 2021).<i>V. vitis-idaea</i> ssp. <i>vitis-idaea</i><i> </i>var. 'Red Candy' scaffolded assembly by mapping to the bilberry genome in fasta format (<i>V. myrtillus</i>; Wu et al. 2021).Annotation of genes/mRNAs associated with the scaffolded genome in gff3 format.Protein sequences from gene annotation in amino acid fasta or faa format.Coding sequences in nucleotide fasta format.Annotation of transposable elements associated with the scaffolded genome in gff3 format.Raw sequences generated in this study are found in NCBI under PRJNA998787: Oxford Nanopore (SRR25468442-SRR25468450), Illumina NovaSeq (SRR25477290)The contig-level assembly fasta can also be found in NCBI: JAUYVE000000000Reference: Wu,C., Deng,C., Hilario,E., Albert,N., Lafferty,D., Plunkett,B., Elborough,C., Saei,A., Jaakola,L., Karppinen,K., Grande,A., Kylli,R., Allan,A., Espley,R. and Chagne,D. 2021. A chromosome-scale assembly of the bilberry genome identifies a complex locus controlling berry anthocyanin composition. Molecular Ecology Resources, DOI 10.1111/1755-0998.13467
DOI: 10.6084/m9.figshare.23928468.v3
title: minus_assembly_dataset

description: Contains seven items:<i>V. vitis-idaea</i> ssp. <i>minus</i> <i>de novo</i> assembly in fasta format.<i>V. vitis-idaea</i> ssp. <i>minus</i> scaffolded assembly by mapping to the bilberry genome in agp format based on contig names in the <i>de novo</i> assembled genome (<i>V. myrtillus</i>; Wu et al. 2021).<i>V. vitis-idaea</i> ssp. <i>minus</i> scaffolded assembly by mapping to the bilberry genome in fasta format (<i>V. myrtillus</i>; Wu et al. 2021).Annotation of genes/mRNAs associated with the scaffolded genome in .gff3 format.Protein sequences from gene annotation in amino acid fasta or faa format.Coding sequences in nucleotide fasta format.Annotation of transposable elements associated with the scaffolded genome in gff3 format.Raw sequences generated in this study are found in NCBI under PRJNA998787: Oxford Nanopore (SRR25468432-SRR25468441), Illumina NovaSeq (SRR25477289)The contig-level assembly fasta can also be found in NCBI: JAUYVF000000000Reference: Wu,C., Deng,C., Hilario,E., Albert,N., Lafferty,D., Plunkett,B., Elborough,C., Saei,A., Jaakola,L., Karppinen,K., Grande,A., Kylli,R., Allan,A., Espley,R. and Chagne,D. 2021. A chromosome-scale assembly of the bilberry genome identifies a complex locus controlling berry anthocyanin composition. Molecular Ecology Resources, DOI 10.1111/1755-0998.13467
DOI: 10.5281/zenodo.10022861
title: Example data for localize-psf
DOI: 10.5281/zenodo.10022862
title: Example data for localize-psf
DOI: 10.6084/m9.figshare.23928468
title: minus_assembly_dataset

description: Contains seven items:<i>V. vitis-idaea</i> ssp. <i>minus</i> <i>de novo</i> assembly in fasta format.<i>V. vitis-idaea</i> ssp. <i>minus</i> scaffolded assembly by mapping to the bilberry genome in agp format based on contig names in the <i>de novo</i> assembled genome (<i>V. myrtillus</i>; Wu et al. 2021).<i>V. vitis-idaea</i> ssp. <i>minus</i> scaffolded assembly by mapping to the bilberry genome in fasta format (<i>V. myrtillus</i>; Wu et al. 2021).Annotation of genes/mRNAs associated with the scaffolded genome in .gff3 format.Protein sequences from gene annotation in amino acid fasta or faa format.Coding sequences in nucleotide fasta format.Annotation of transposable elements associated with the scaffolded genome in gff3 format.Raw sequences generated in this study are found in NCBI under PRJNA998787: Oxford Nanopore (SRR25468432-SRR25468441), Illumina NovaSeq (SRR25477289)The contig-level assembly fasta can also be found in NCBI: JAUYVF000000000Reference: Wu,C., Deng,C., Hilario,E., Albert,N., Lafferty,D., Plunkett,B., Elborough,C., Saei,A., Jaakola,L., Karppinen,K., Grande,A., Kylli,R., Allan,A., Espley,R. and Chagne,D. 2021. A chromosome-scale assembly of the bilberry genome identifies a complex locus controlling berry anthocyanin composition. Molecular Ecology Resources, DOI 10.1111/1755-0998.13467