cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.18783948
title: Raw data and data accompanying publication: https://doi.org/10.1261/rna.080367.124

description: Raw data and data accompanying publication:

Angelo M., Bhargava Y., Kierzek E., Kierzek R., Hayes R.L., Zhang W., Vilseck J.Z., Aoki S.T., Accurate in silico predictions of modified RNA interactions to a prototypical RNA-binding protein with λ-dynamics. RNA (2025) 31(10), 1460-1471. https://doi.org/10.1261/rna.080367.124

Authors: Murphy Angelo (1), Yash Bhargava (1), Elzbieta Kierzek (2), Ryszard Kierzek (2), Ryan L Hayes (3,4), Wen Zhang* (1,5), Jonah Z Vilseck* (1,6), Scott Takeo Aoki* (1,5)

Affiliation:(1) Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA(2) Institute of Bioorganic Chemistry Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland(3) Department of Chemical and Biomolecular Engineering, University of California Irvine, Irvine, California 92697, USA(4) Department of Pharmaceutical Sciences, University of California Irvine, Irvine, California 92697, USA(5) Melvin and Bren Simon Cancer Center, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA(6) Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA

* Corresponding authors: E-mails: wz15@iu.edu, jvilseck@iu.edu, staoki@iu.edu

License:  CC BY-NC 4.0

This work was supported by: S.T.A., W.Z., and J.Z.V. received startup funds from the Indiana University School of Medicine and its Precision Health Initiative (PHI). J.Z.V. is funded by the National Institute of General Medical Sciences (NIGMS) of the National Institutes of Health (NIH) (R35GM146888). S.T.A. is funded by the NIH/NIGMS (R35GM142691) and an Indiana University Research Support Funds Grant (RSFG). E.K. is funded by UMO-2020/39/B/NZ1/03054 and R.K. is funded by UMO-2022/45/B/ST4/03586.

Contents:Data1: Legends.Data2: Figure S1- ANOVA binding statistics.Data3: Figure S2- Human Pumilio 2 binding to modified RNAs.Data4: Figure S3- A thermodynamic cycle used for computing relative binding free energies (ΔΔGbind).Data5: Table S1- Human Pumilio 1 and 2 λ-dynamics screening results to unmodified RNA. Data6: Table S2- Human Pumilio 1 λ-dynamics screening results to modified RNA. Data7: Table S3- Human Pumilio 2 λ-dynamics and in vitro binding results to modified RNA. Data8: Table S4- Alchemical groups for initial λ-dynamics screen of modified RNA bases.
DOI: 10.13018/bmr18541
title: NMR solution structure of midkine-b, mdkb
DOI: 10.13018/bmr18542
title: Structure and Binding Interface of the Cytosolic Tails of aXb2 Integrin
DOI: 10.13018/bmr18543
title: Chemical shift assignments of DsbA(C33S) by solid-state NMR
DOI: 10.13018/bmr18544
title: Chemical shift assignments of DsbA(C33S)/DsbB by solid-state NMR
DOI: 10.13018/bmr18545
title: Calcium saturated form of human C85M S100A1 mutant
DOI: 10.13018/bmr18546
title: Solution structure of the tandem zinc finger domain of fission yeast Stc1
DOI: 10.15468/dl.7ku6y3
title: Occurrence Download

description: A dataset containing 142030 records in GBIF matching the query:
SELECT
 kingdom,
 kingdomkey,
 phylum,
 phylumkey,
 class,
 classkey,
 "order",
 orderkey,
 family,
 familykey,
 genus,
 genuskey,
 species,
 specieskey,
 "year",
 IF(ISNULL(kingdomkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY kingdomkey, "year")) kingdomcount,
 IF(ISNULL(phylumkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY phylumkey, "year")) phylumcount,
 IF(ISNULL(classkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY classkey, "year")) classcount,
 IF(ISNULL(orderkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY orderkey, "year")) ordercount,
 IF(ISNULL(familykey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY familykey, "year")) familycount,
 IF(ISNULL(genuskey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY genuskey, "year")) genuscount,
 COUNT(*) occurrences,
 MIN(GBIF_TEMPORALUNCERTAINTY(eventdate, eventtime)) mintemporaluncertainty,
 MIN(COALESCE(coordinateuncertaintyinmeters, 1000)) mincoordinateuncertaintyinmeters
FROM
 occurrence
WHERE
 occurrence.countrycode = 'ID'
 AND occurrence.occurrencestatus = 'PRESENT'
 AND (occurrence."year" &gt;= 1999 AND occurrence."year" &lt;= 2026)
 AND occurrence.hasgeospatialissues = FALSE
 AND NOT GBIF_STRINGARRAYCONTAINS(occurrence.issue, 'TAXON_MATCH_FUZZY', TRUE)
 AND (occurrence.distancefromcentroidinmeters &gt;= 2000.0 OR occurrence.distancefromcentroidinmeters IS NULL)
 AND NOT occurrence.basisofrecord IN ('FOSSIL_SPECIMEN', 'LIVING_SPECIMEN')
 AND (occurrence.classificationdetails['d7dddbf4-2cf0-4f39-9b2a-bb099caae36c']['specieskey'] &lt;&gt; '' AND occurrence."year" IS NOT NULL)
GROUP BY
 occurrence.kingdom,
 occurrence.kingdomkey,
 occurrence.phylum,
 occurrence.phylumkey,
 occurrence.class,
 occurrence.classkey,
 occurrence."order",
 occurrence.orderkey,
 occurrence.family,
 occurrence.familykey,
 occurrence.genus,
 occurrence.genuskey,
 occurrence.species,
 occurrence.specieskey,
 occurrence."year"

 The dataset's 142030 records were derived from 927 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003170-260225131425191/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5517/cc46zx6
title: CCDC 125888: Experimental Crystal Structure Determination

description: Related Article: D.M.C.Chan, C.H.Schwalbe, G.Sood, W.Fraser|1995|Acta Crystallogr.,Sect.C:Cryst.Struct.Commun.|51|2383|doi:10.1107/S0108270195008705
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/cc4711f
title: CCDC 125923: Experimental Crystal Structure Determination

description: Related Article: I.Alonso, I.Lopez-Solera, P.R.Raithby|1995|Acta Crystallogr.,Sect.C:Cryst.Struct.Commun.|51|2381|doi:10.1107/S0108270195006214
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/cc470n0
title: CCDC 125911: Experimental Crystal Structure Determination

description: Related Article: Rajnikant, D.J.Watkin, G.Tranter|1995|Acta Crystallogr.,Sect.C:Cryst.Struct.Commun.|51|2388|doi:10.1107/S0108270195006329
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/cc472cs
title: CCDC 125964: Experimental Crystal Structure Determination

description: Related Article: B.C.Das, S.Pain Biswas, G.Biswas, S.N.Ganguly, A.Banerjee, W.L.Duax, B.B.Maji, K.L.Ghatak|1995|Acta Crystallogr.,Sect.C:Cryst.Struct.Commun.|51|2386|doi:10.1107/S0108270195004872
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/cc46zcn
title: CCDC 125871: Experimental Crystal Structure Determination

description: Related Article: S.Zaitu, Y.Miwa, T.Taga|1995|Acta Crystallogr.,Sect.C:Cryst.Struct.Commun.|51|2390|doi:10.1107/S010827019500864X
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/cc46zhs
title: CCDC 125875: Experimental Crystal Structure Determination

description: Related Article: J.Bolger, A.Gourdon|1995|Acta Crystallogr.,Sect.C:Cryst.Struct.Commun.|51|2395|doi:10.1107/S0108270195006950
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: 10.15468/dl.xyakks
title: Occurrence Download

description: A dataset containing 32 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is (Table 1) Proportion of Toxoplasma gondii seropositive arctic foxes (Alopex lagopus) by age group and geographic area"
 ]
}

 The dataset includes 32 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007653-180730143533302/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kret4p
title: Occurrence Download

description: A dataset containing 151 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Heliolonche Grote, 1873"
 ]
}

 The dataset includes 151 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0258543-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pnanc2
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is (Table 1) Proportion of Toxoplasma gondii seropositive arctic foxes (Alopex lagopus) by age group and geographic area"
 ]
}

 The dataset includes 8 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0041264-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wuzkfk
title: Occurrence Download

description: A dataset containing 41336771 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Norway",
 "Year 1852-2021"
 ]
}

 The dataset includes 41336771 records from 1109 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0254475-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.58iycv
title: Occurrence Download

description: A dataset containing 32 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is (Table 1) Proportion of Toxoplasma gondii seropositive arctic foxes (Alopex lagopus) by age group and geographic area"
 ]
}

 The dataset includes 32 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007809-180730143533302/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.chvqu5
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is (Table 1) Proportion of Toxoplasma gondii seropositive arctic foxes (Alopex lagopus) by age group and geographic area"
 ]
}

 The dataset includes 8 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0053750-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.scuxt3
title: Occurrence Download

description: A dataset containing 28 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((3.01684 39.91126,3.21734 39.91126,3.21734 39.99142,3.01684 39.99142,3.01684 39.91126))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Brimeura duvigneaudii (L.Llorens) Rosselló, Mus & Mayol"
 ]
}

 The dataset includes 28 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0253628-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ka7s33
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is (Table 1) Proportion of Toxoplasma gondii seropositive arctic foxes (Alopex lagopus) by age group and geographic area"
 ]
}

 The dataset includes 8 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0041360-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5gawdg
title: Occurrence Download

description: A dataset containing 32 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is (Table 1) Proportion of Toxoplasma gondii seropositive arctic foxes (Alopex lagopus) by age group and geographic area"
 ]
}

 The dataset includes 32 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007700-180730143533302/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5fsswv
title: Occurrence Download

description: A dataset containing 26023427 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is iNaturalist Research-grade Observations"
 ]
}

 The dataset includes 26023427 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0253881-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6kckn9
title: Occurrence Download

description: A dataset containing 32 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is (Table 1) Proportion of Toxoplasma gondii seropositive arctic foxes (Alopex lagopus) by age group and geographic area"
 ]
}

 The dataset includes 32 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007782-180730143533302/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9igtij
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is (Table 1) Proportion of Toxoplasma gondii seropositive arctic foxes (Alopex lagopus) by age group and geographic area"
 ]
}

 The dataset includes 8 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0041267-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2qlyne
title: Occurrence Download

description: A dataset containing 32 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is (Table 1) Proportion of Toxoplasma gondii seropositive arctic foxes (Alopex lagopus) by age group and geographic area"
 ]
}

 The dataset includes 32 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007732-180730143533302/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.oew2fr
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is (Table 1) Proportion of Toxoplasma gondii seropositive arctic foxes (Alopex lagopus) by age group and geographic area"
 ]
}

 The dataset includes 8 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0041268-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.elksac
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is (Table 1) Proportion of Toxoplasma gondii seropositive arctic foxes (Alopex lagopus) by age group and geographic area"
 ]
}

 The dataset includes 8 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0041280-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.0ciky0
title: Occurrence Download

description: A dataset containing 32 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is (Table 1) Proportion of Toxoplasma gondii seropositive arctic foxes (Alopex lagopus) by age group and geographic area"
 ]
}

 The dataset includes 32 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007888-180730143533302/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.r5gkvp
title: Occurrence Download

description: A dataset listing the 19363 species recorded in GBIF matching the query:
{
 "and" : [
 "Country is Cameroon",
 "OccurrenceStatus is Present",
 "TaxonKey is Plantae"
 ]
}

 The dataset's 19363 records were derived from 254 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003868-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60712/si-id44716.1
title: StrainInfo SI-ID 44716.1

description: StrainInfo dataset 44716 about a strain of Pseudomonas aeruginosa. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id44717.1
title: StrainInfo SI-ID 44717.1

description: StrainInfo dataset 44717 about a strain of Pseudomonas aeruginosa. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id44718.1
title: StrainInfo SI-ID 44718.1

description: StrainInfo dataset 44718 about a strain of Nitrobacter. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id44719.1
title: StrainInfo SI-ID 44719.1

description: StrainInfo dataset 44719 about a strain of Listeria grayi. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id44809.1
title: StrainInfo SI-ID 44809.1

description: StrainInfo dataset 44809 about a strain of Streptomyces peucetius. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id44810.1
title: StrainInfo SI-ID 44810.1

description: StrainInfo dataset 44810 about a strain of Bacillus subtilis. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id44811.1
title: StrainInfo SI-ID 44811.1

description: StrainInfo dataset 44811 about a strain of Mesomycoplasma bovoculi. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id44812.1
title: StrainInfo SI-ID 44812.1

description: StrainInfo dataset 44812 about a strain of Gloeocapsa. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.15468/dl.ttmwy9
title: Occurrence Download

description: A dataset containing 563996 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Australia",
 "TaxonKey is Strepera graculina (Shaw, 1790)"
 ]
}

 The dataset includes 563996 records from 94 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0165489-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60712/si-id44874.1
title: StrainInfo SI-ID 44874.1

description: StrainInfo dataset 44874 about a strain of Bacillus subtilis. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id44875.1
title: StrainInfo SI-ID 44875.1

description: StrainInfo dataset 44875 about a strain of Streptomyces hygroscopicus subsp. hygroscopicus. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id44876.1
title: StrainInfo SI-ID 44876.1

description: StrainInfo dataset 44876 about a strain of Corynebacterium. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id44877.1
title: StrainInfo SI-ID 44877.1

description: StrainInfo dataset 44877 about a strain of Bacillus subtilis. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id44720.1
title: StrainInfo SI-ID 44720.1

description: StrainInfo dataset 44720 about a strain of Streptomyces. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id44722.1
title: StrainInfo SI-ID 44722.1

description: StrainInfo dataset 44722 about a strain of Eggerthella lenta. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.