cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.18299233
title: Data for the manuscript : "Structural basis of signal peptide recognition by the signal peptidase complex"

description: Supplementary Data generated during the Molecular Dynamics simulations and AlphaFold2-multimer modeling employed for the manuscript: "Structural basis of signal peptide recognition by the signal peptidase complex" by Liaci, Vismpas et al., 2026.

 

This repository contains:

1) MD.zip: MD trajectory data with the following folders and file:



PDF with additional SI figures for the MD simulations.



AA (atomistic): APO, L11, P08514, POPC — topology and parameter files.




CG (coarse-grained): APO, L11 — topology and parameter files.




Raw_plots: Additional SI figures.



2) generated_af2m_sp_models.zip: Alphafold2-multimer models of 412 curated human signal peptide sequences in complex with Sec11A, along with quality plots.

3) accepted_sp_models.zip: Accepted AF2-m models after filtering.

4) PQR file used to determine the protonation states of the protein complex.
DOI: 10.5281/zenodo.18299232
title: Data for the manuscript : "Structural basis of signal peptide recognition by the signal peptidase complex"

description: Supplementary Data generated during the Molecular Dynamics simulations and AlphaFold2-multimer modeling employed for the manuscript: "Structural basis of signal peptide recognition by the signal peptidase complex" by Liaci, Vismpas et al., 2026.

 

This repository contains:

1) MD.zip: MD trajectory data with the following folders and file:



PDF with additional SI figures for the MD simulations.



AA (atomistic): APO, L11, P08514, POPC — topology and parameter files.




CG (coarse-grained): APO, L11 — topology and parameter files.




Raw_plots: Additional SI figures.



2) generated_af2m_sp_models.zip: Alphafold2-multimer models of 412 curated human signal peptide sequences in complex with Sec11A, along with quality plots.

3) accepted_sp_models.zip: Accepted AF2-m models after filtering.

4) PQR file used to determine the protonation states of the protein complex.
DOI: 10.48580/d3ljc.v187
title: Taxon list of Megaloptera from Germany compiled in the context of the GBOL project
DOI: 10.48580/d3c8z.v143
title: A checklist of invertebrates of Ewaso Narok swamp in the semi-arid Laikipia County, Kenya
DOI: 10.15468/dl.cvrnuv
title: Occurrence Download

description: A dataset containing 2721 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "DistanceFromCentroidInMeters is greater than or equal to 2000",
 "TaxonKey is Lutjanus viridis"
 ]
}

 The dataset includes 2721 records from 56 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007145-260221153910048/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.48580/d45hs.v187
title: Taxon list of liverworts from Germany compiled in the context of the GBOL project
DOI: 10.48580/d389c.v142
title: A Checklist of the Birds of Arabuko-Sokoke Forest, Kenya
DOI: 10.48580/d3kh7.v187
title: Taxon list of Thysanoptera from Germany compiled in the context of the GBOL project
DOI: 10.48580/d45ht.v189
title: Taxon list of hornworts from Germany compiled in the context of the GBOL project
DOI: 10.48580/d3l4l.v188
title: Taxon list of Raphidioptera from Germany compiled in the context of the GBOL project
DOI: 10.48580/d3lqt.v190
title: Taxon list of Symphyla from Germany compiled in the context of the GBOL project
DOI: 10.48580/dfhg.v142
title: A preliminary checklist of some insects (Coleoptera, Odonata, Hymenoptera) from Arabuko-Sokoke Forest, Kenya
DOI: 10.48580/d47z7.v104
title: A checklist of birds of Anwase forest
DOI: 10.48580/d4d9w.v144
title: Checklist of Butterflies of Shimba Hills and the southern Kenya Coastal landscapes, 1957 to 2020
DOI: 10.48580/d3dm3.v189
title: Taxon list of Dictyoptera from Germany compiled in the context of the GBOL project
DOI: 10.48580/d3lqs.v188
title: Taxon list of Diplura from Germany compiled in the context of the GBOL project
DOI: 10.48580/dfsbj.v6
title: Updated checklist of the ants in Belgium
DOI: 10.48580/d3725.v144
title: A checklist of the reptiles and amphibians of Arabuko-Sokoke Forest, Kenya, 2019
DOI: 10.48580/d36yc.v142
title: A checklist of plants of Arabuko-Sokoke Forest, Kenya, 2019
DOI: 10.48580/d36xt.v9
title: Validated red lists of Flanders, Belgium
DOI: 10.15468/dl.exz5te
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Armenia",
 "TaxonKey is Galerina marginata"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007148-260221153910048/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.uv87w3
title: Occurrence Download

description: A dataset containing 141971 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Leptotila verreauxi",
 "Country is Colombia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 141971 records from 442 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007060-260221153910048/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.awvsdu
title: Occurrence Download

description: A dataset containing 100059 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Momotus aequatorialis",
 "Year is greater than or equal to 2000",
 "Year is less than or equal to 2026",
 "Country is Colombia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 100059 records from 145 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007104-260221153910048/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.48544/586c65c5-00f3-43a1-83cb-c14e60ecd41c
title: Van het gas af wordt makkelijker
DOI: 10.15468/dl.w76cgv
title: Occurrence Download

description: A dataset containing 10 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cyperus cancellatus Ridl."
 ]
}

 The dataset includes 10 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017444-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rigy4j
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/0028940-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.auw6ee
title: Occurrence Download

description: A dataset containing 1940 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pareuchaetes insulata Walker, 1855"
 ]
}

 The dataset includes 1940 records from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0190599-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.f26skp
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/0003450-180824113759888/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.he4q9g
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/0028927-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hvzegf
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cyrtandra jellesmani Koord."
 ]
}

 The dataset includes 2 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017457-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.iscmtk
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/0040621-180508205500799/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.r6wzjr
title: Occurrence Download

description: A dataset containing 27 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pseudocharis Druce, 1884"
 ]
}

 The dataset includes 27 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0190610-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sscpy7
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/0028917-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2z9qet
title: Occurrence Download

description: A dataset containing 689 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cyperus capillifolius A.Rich."
 ]
}

 The dataset includes 689 records from 85 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017461-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.km3y6b
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Thailand",
 "DatasetKey is iNaturalist Research-grade Observations",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Stichopus herrmanni Semper, 1868",
 "Year 2000-2024"
 ]
}

 The dataset includes 6 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0072061-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.exdf7j
title: Occurrence Download

description: A dataset containing 71 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pygarctia abdominalis Grote, 1871"
 ]
}

 The dataset includes 71 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0190616-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vdoylb
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/0029003-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4wsedp
title: Occurrence Download

description: A dataset containing 27 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cyrtandra jonesii (F.Br.) G.W.Gillett"
 ]
}

 The dataset includes 27 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017465-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ceudsu
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pygarctia elegans"
 ]
}

 The dataset includes 2 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0190618-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.thab3s
title: Occurrence Download

description: A dataset containing 917853829 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 917853829 records from 16906 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0040481-180508205500799/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25921/xbrf-wb02
title: NOAA/WDS Paleoclimatology - Zumbrunn - Felsberg oben - PCAB - ITRDB CHE510

description: Tree ring data from the International Tree Ring Data Bank and World Data Center for Paleoclimatology archives.  Most data sets include raw treering measurements (most are annual ring width, with some collections of earlywood or latewood width or wood density), plus chronologies (standardized growth indices for a site compiled from multiple treering samples). Reconstructions of climate variables are included with some of these data sets.  Each data type is stored in a separate data file; the data type is coded into the file name. For details please see: http://www.ncdc.noaa.gov/paleo/treeinfo.htmll
DOI: 10.5517/cc8t1tx
title: CCDC 262409: Experimental Crystal Structure Determination

description: Related Article: W.Kaim, C.Titze, T.Schurr, M.Sieger, M.Lawson, J.Jordanov, D.Rojas, A.M.Garcia, J.Manzur|2005|Z.Anorg.Allg.Chem.|631|2568|doi:10.1002/zaac.200500053
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/cc8sp5w
title: CCDC 262048: Experimental Crystal Structure Determination

description: Related Article: E.-M.Zerbe, P.G.Jones, O.Moers, A.Blaschette|2005|Z.Anorg.Allg.Chem.|631|2623|doi:10.1002/zaac.200500056
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: 10.25921/xtz0-be89
title: NOAA/WDS Paleoclimatology - Weber - BAT - FASY - ITRDB CHE582

description: Tree ring data from the International Tree Ring Data Bank and World Data Center for Paleoclimatology archives.  Most data sets include raw treering measurements (most are annual ring width, with some collections of earlywood or latewood width or wood density), plus chronologies (standardized growth indices for a site compiled from multiple treering samples). Reconstructions of climate variables are included with some of these data sets.  Each data type is stored in a separate data file; the data type is coded into the file name. For details please see: http://www.ncdc.noaa.gov/paleo/treeinfo.htmll
DOI: 10.5517/cc9g945
title: CCDC 281856: Experimental Crystal Structure Determination

description: Related Article: S.Schwieger, C.Wagner, C.Bruhn, H.Schmidt, D.Steinborn|2005|Z.Anorg.Allg.Chem.|631|2696|doi:10.1002/zaac.200500110
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/cc9g956
title: CCDC 281857: Experimental Crystal Structure Determination

description: Related Article: S.Schwieger, C.Wagner, C.Bruhn, H.Schmidt, D.Steinborn|2005|Z.Anorg.Allg.Chem.|631|2696|doi:10.1002/zaac.200500110
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: 10.25921/x97m-sf41
title: NOAA/WDS Paleoclimatology - Nehrbass-Ahles - Vordemwald Update - QURO - ITRDB CHE592

description: Tree ring data from the International Tree Ring Data Bank and World Data Center for Paleoclimatology archives.  Most data sets include raw treering measurements (most are annual ring width, with some collections of earlywood or latewood width or wood density), plus chronologies (standardized growth indices for a site compiled from multiple treering samples). Reconstructions of climate variables are included with some of these data sets.  Each data type is stored in a separate data file; the data type is coded into the file name. For details please see: http://www.ncdc.noaa.gov/paleo/treeinfo.htmll
DOI: 10.5517/cc8v38g
title: CCDC 263415: Experimental Crystal Structure Determination

description: Related Article: R.Haiges, T.Schroer, M.Yousufuddin, K.O.Christe|2005|Z.Anorg.Allg.Chem.|631|2691|doi:10.1002/zaac.200500289
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/cc9g967
title: CCDC 281858: Experimental Crystal Structure Determination

description: Related Article: S.Schwieger, C.Wagner, C.Bruhn, H.Schmidt, D.Steinborn|2005|Z.Anorg.Allg.Chem.|631|2696|doi:10.1002/zaac.200500110
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: 10.25921/x5hg-kh28
title: NOAA/WDS Paleoclimatology - Villars Cave, Chauvet Cave, La Mine Cave Geochemical Data from 34200 to 5300 Cal Yr BP

description: The last deglaciation and its climatic events, such as the Bølling–Allerød (BA) and the Younger–Dryas (YD), have been clearly recorded in the δ13C profiles of three stalagmites from caves from Southern France to Northern Tunisia. The three δ13C records, dated by thermal ionization mass spectrometric uranium–thorium method (TIMS), show great synchroneity and similarity in shape with the Chinese cave δ18O records and with the marine tropical records, leading to the hypothesis of an in-phase (between 15.5 and 16 ka ∼±0.5 ka) postglacial warming in the Northern Hemisphere, up to at least 45°N. The BA transition appears more gradual in the speleothem records than in the Greenland records and the Allerød seems warmer than the Bølling, showing here close similarities with other marine and continental archives. A North–South gradient is observed in the BA trend: it cools in Greenland and warms in our speleothem records. Several climatic events are clearly recognizable: a cooler period at about 14 ka (Older Dryas (OD)); the Intra-Allerød Cold Period at about ∼13.3 ka; the YD cooling onset between 12.7 and 12.9±0.3 ka. Similar to the BA, the YD displays a gradual climate amelioration just after its onset at 12.75±0.25 ka, up to the Preboreal, and is punctuated by a short climatic event at 12.15 ka. Even though the Southern Hemisphere stalagmite records seem to indicate that the postglacial warming started about ∼3 ka±1.8 ka earlier in New Zealand (∼41 °S), and about ∼1 to ∼2 ka earlier in South Africa (24.1 °S), large age uncertainties, essentially due to slow growth rates, make the comparison still perilous. The overall δ13C speleothem record seems to follow a baseline temperature increase controlled by the increase in insolation and punctuated by cold events possibly due to the N-America freshwater lake discharges.
description: Data contributed as part of SISAL v3 Global Speleothem Isotope and Trace Element Database (https://doi.org/10.25921/jajq-qg60). Notes from the SISAL database: Vegetation: Mediterranean composed of small bushes and sparse green oaks. \\ Chau-stm6 (SISAL entity_id=166): Detrital Th correction not made in original publication and therefore initial Th data is not existent. U-Th ages for entity_id=166 were calculated using the following decay constants: 234U: 2.835*10^(-6)/yr, 238U: 1.55125*10^(-10)/yr, 230Th: 9.1952*10^(-6)/yr, 232Th: 4.9475*10^(-11)/yr. Decay constants are probably derived from the following papers: 230Th: Meadows et al.,1980, 234U: average value from De Bievre et al. 1971 and Lounsbury and Durham 1971.
DOI: 10.5517/cc8v39h
title: CCDC 263416: Experimental Crystal Structure Determination

description: Related Article: R.Haiges, T.Schroer, M.Yousufuddin, K.O.Christe|2005|Z.Anorg.Allg.Chem.|631|2691|doi:10.1002/zaac.200500289
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.