cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.13362096
title: Data for 'Ranking Single Fluorescent Protein Based Calcium Biosensor Performance by Molecular Dynamics Simulations'

description: Melike Berksoz, Canan Atilgan* 

Faculty of Engineering and Natural Sciences, Sabanci University 

*Correspondance: Canan Atilgan, Faculty of Natural Sciences and Engineering, Sabancı University, Tuzla 34956 Istanbul, Türkiye, E-mail: canan@sabanciuniv.edu

Genetically Encoded Fluorescent Biosensors (GEFBs) have become indispensable tools for visualizing biological processes in vivo. A typical GEFB is composed of a sensory domain (SD) which undergoes a conformational change upon ligand binding and a genetically fused fluorescent protein (FP). Ligand binding in the SD allosterically modulates the chromophore environment and changes its spectral properties. Single fluorescent (FP)-based biosensors, a subclass of GEFBs, offer a simple experimental setup; they are easy to produce in living cells, structurally stable and simple due to their single-wavelength operation. However, they pose a significant challenge for structure optimization, especially concerning the length and residue content of linkers between the FP and SD which effect how well the chromophore responds to conformational change in the SD. In this work, we use classical all-atom molecular dynamics simulations to analyze the dynamic properties of a series of calmodulin-based calcium biosensors, all with different FP-SD interaction interfaces and varying degrees of calcium binding dependent fluorescence change. Our results indicate that biosensor performance can be predicted based on distribution of water molecules around the chromophore and shifts in hydrogen bond occupancies between the ligand-bound and ligand-free sensor structures.

Hydrogen bond occupancies were calculated with merging_bonds.py script. Double counted hydrogen bonds where a residue acts both as acceptor and donor are merged into a single entry with merge_files.py. To run sasa.tcl, you need VMD software. Trajectories were created with NAMD2 with a dcdfrequency of 5000 timesteps (every 10 ps) and strided in a 1:100 ratio (every 1 ns=1 frame in dcd).
DOI: 10.5281/zenodo.14199597
title: Data for 'Ranking Single Fluorescent Protein Based Calcium Biosensor Performance by Molecular Dynamics Simulations'

description: Melike Berksoz, Canan Atilgan* 

Faculty of Engineering and Natural Sciences, Sabanci University 

*Correspondance: Canan Atilgan, Faculty of Natural Sciences and Engineering, Sabancı University, Tuzla 34956 Istanbul, Türkiye, E-mail: canan@sabanciuniv.edu

Genetically Encoded Fluorescent Biosensors (GEFBs) have become indispensable tools for visualizing biological processes in vivo. A typical GEFB is composed of a sensory domain (SD) which undergoes a conformational change upon ligand binding and a genetically fused fluorescent protein (FP). Ligand binding in the SD allosterically modulates the chromophore environment and changes its spectral properties. Single fluorescent (FP)-based biosensors, a subclass of GEFBs, offer a simple experimental setup; they are easy to produce in living cells, structurally stable and simple due to their single-wavelength operation. However, they pose a significant challenge for structure optimization, especially concerning the length and residue content of linkers between the FP and SD which effect how well the chromophore responds to conformational change in the SD. In this work, we use classical all-atom molecular dynamics simulations to analyze the dynamic properties of a series of calmodulin-based calcium biosensors, all with different FP-SD interaction interfaces and varying degrees of calcium binding dependent fluorescence change. Our results indicate that biosensor performance can be predicted based on distribution of water molecules around the chromophore and shifts in hydrogen bond occupancies between the ligand-bound and ligand-free sensor structures.

Hydrogen bond occupancies were calculated with merging_bonds.py script. Double counted hydrogen bonds where a residue acts both as acceptor and donor are merged into a single entry with merge_files.py. To run sasa.tcl, you need VMD software. Trajectories were created with NAMD2 with a dcdfrequency of 5000 timesteps (every 10 ps) and strided in a 1:100 ratio (every 1 ns=1 frame in dcd).
DOI: 10.5518/1375
title: Data to support 'Ephemeral Ice Clouds in the Upper Mesosphere of Venus' 

description: This dataset contains the the data and codes associated with 'Ephemeral Ice Clouds in the Upper Mesosphere of Venus'. This is a theoretical study of properties of clouds that may form in the upper atmosphere of Venus.
DOI: 10.15468/dl.bd62w5
title: Occurrence Download

description: A dataset containing 201 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)"
 ]
 }
 },
 "TaxonKey is one of (Indocalamus latifolius (Keng) McClure)"
 ]
}

 The dataset includes 201 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004712-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.s2tvc4
title: Occurrence Download

description: A dataset containing 471030 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "GadmGid is ITA",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 471030 records from 777 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0040708-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.18738/t8/co5tgn
title: Carta real sobre el establecimiento de misiones en Coahuila y Texas, 1690 septiembre 20
title: Royal letter on the establishment of missions in Coahuila and Texas, 1690 September 20

description: Respuesta real al obispo Juan de Santiago de León Garavito de Guadalajara, quien había informado sobre el “descubrimiento” de numerosas poblaciones indígenas en la provincia de Coahuila y regiones cercanas. El rey reconoce la propuesta del obispo de organizar esfuerzos misioneros entre los grupos indígenas conocidos como los “Texas”, descritos como más políticamente organizados y receptivos al cristianismo que otros. El monarca elogia el celo del obispo y le informa que el virrey de la Nueva España ya ha recibido instrucciones de continuar y ampliar la labor misional, especialmente mediante el envío de frailes franciscanos para establecer cinco o seis misiones con fondos reales. —— Royal response to Bishop Juan de Santiago de León Garavito of Guadalajara, who had reported on the 'discovery' of numerous Indigenous populations in the Province of Coahuila and nearby regions. The king acknowledges the bishop’s proposal to organize missionary efforts among the Indigenous groups known as the 'Texas', described as more politically organized and receptive to Christianity than others. The monarch praises the bishop’s zeal and informs him that the Viceroy of New Spain has already been instructed to continue and expand missionary work, especially by sending Franciscan friars to establish five or six missions with royal funds. 2 f. (4 p.)
description: FromThePage, 21.9
description: Maria Monte transcribió este documento del 6 al 8 de septiembre de 2018 a través de la plataforma FromThePage de las Bibliotecas de la Universidad de Texas. Albert A. Palacios corrigio, finalizo y exporto las transcripciones de FromThePage el 7 de octubre de 2025. El manuscrito esta clasificado como WBS 2031 en la Colección William B. Stephens, Benson Latin American Collection, LLILAS Benson Latin American Studies and Collections, The University of Texas en Austin. —— Maria Monte transcribed document on 2018 September 6-8 through UT Libraries' FromThePage instance. Albert A. Palacios corrected, finalized, and exported the FromThePage transcriptions on 2025 October 7. Item is WBS 2031 in the William B. Stephens Collection, Benson Latin American Collection, LLILAS Benson Latin American Studies and Collections, The University of Texas at Austin.
DOI: 10.15468/dl.hgtqh2
title: Occurrence Download

description: A dataset containing 11 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((29.98533 0.3577,29.98987 0.29764,30.13352 0.22019,30.14374 0.24607,30.13497 0.27591,30.10772 0.34956,30.02324 0.37857,29.98533 0.3577))",
 "TaxonKey is one of (Lantana camara L., Senna spectabilis (DC.) H.S.Irwin & Barneby, Senna siamea (Lam.) H.S.Irwin & Barneby)"
 ]
}

 The dataset includes 11 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020387-250402121839773/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25582/data.2024-04.3091185/2557799
title: Data for EMSL Project 51287 from April 2024
DOI: 10.25582/data.2024-04.3091186/2557800
title: Data for EMSL Project 51287 from April 2024
DOI: 10.25582/data.2024-04.3091187/2557801
title: Data for EMSL Project 51287 from April 2024
DOI: 10.25582/data.2024-04.3091188/2557802
title: Data for EMSL Project 51287 from April 2024
DOI: 10.25582/data.2024-04.3091189/2557803
title: Data for EMSL Project 51287 from April 2024
DOI: 10.25582/data.2024-04.3091190/2557804
title: Data for EMSL Project 51287 from April 2024
DOI: 10.25582/data.2024-04.3091191/2557805
title: Data for EMSL Project 51287 from April 2024
DOI: 10.5683/sp2/3rtcyf
title: Modelling the Potential Impacts of Climate Change on Arboreal Diversity of the University of British Columbia Vancouver Campus from 2050 to 2080

description: Climate change poses a considerable risk to forest diversity in urban communities. The University of British Columbia (UBC) seeks to identify vulnerable tree species on campus and apply strategies for sustaining arboreal diversity in future decades. In contribution to these efforts, this study investigated the potential shift in tree composition on the UBC Vancouver Campus over the next century by (1) predicting suitable climatic habitat for 128 campus species in 2050 and 2080, and (2) mapping the expected change in species richness across North America. Species observation data from the Global Biodiversity Information Facility (GBIF) and climate predictors from ClimateNA were used to perform MaxEnt species distribution modelling. The climatic baseline (1961-1990) range for each tree species was defined using average annual temperature and precipitation, and projected using RCP 8.5 climate scenarios for 2050 (2041-2070) and 2080 (2071-2100). This dataset contains all geoprocessing scripts, species range and diversity maps for the baseline year, 2050 and 2080, as well as model outputs for each tree species.
description: ArcGIS Pro, 2.7.1
description: R, 4.0.2
DOI: 10.25582/data.2024-04.3091192/2557806
title: Data for EMSL Project 51287 from April 2024
DOI: 10.5517/cc10qh5d
title: CCDC 945133: Experimental Crystal Structure Determination

description: Related Article: Wei-Tsung Lee,  Diane A. Dickie,  Alejandro J. Metta-Magaña,  and Jeremy M. Smith|2013|Inorg.Chem.|52|12842|doi:10.1021/ic402311c
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/ccywv5t
title: CCDC 890697: Experimental Crystal Structure Determination

description: Related Article: An D. Nguyen,  M. Diego Rail,  Maheswaran Shanmugam,  James C. Fettinger,  and Louise A. Berben|2013|Inorg.Chem.|52|12847|doi:10.1021/ic4023882
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/cc10qh4c
title: CCDC 945132: Experimental Crystal Structure Determination

description: Related Article: Wei-Tsung Lee,  Diane A. Dickie,  Alejandro J. Metta-Magaña,  and Jeremy M. Smith|2013|Inorg.Chem.|52|12842|doi:10.1021/ic402311c
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/cc11rz6z
title: CCDC 976351: Experimental Crystal Structure Determination

description: Related Article: Daniel J. Meininger,  Jonathan D. Caranto,  Hadi D. Arman,  and Zachary J. Tonzetich|2013|Inorg.Chem.|52|12468|doi:10.1021/ic401467k
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/cc11s3xv
title: CCDC 976497: Experimental Crystal Structure Determination

description: Related Article: Wei-Tsung Lee,  Diane A. Dickie,  Alejandro J. Metta-Magaña,  and Jeremy M. Smith|2013|Inorg.Chem.|52|12842|doi:10.1021/ic402311c
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: 10.13140/rg.2.2.22157.24805
title: Aktivitas Bisnis Internasional PROGRAM STUDI MANAJEMEN
DOI: 10.5517/cc11rz70
title: CCDC 976352: Experimental Crystal Structure Determination

description: Related Article: Daniel J. Meininger,  Jonathan D. Caranto,  Hadi D. Arman,  and Zachary J. Tonzetich|2013|Inorg.Chem.|52|12468|doi:10.1021/ic401467k
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: 10.13140/rg.2.2.18811.63521
title: Going the Distance: Advancing Open and Distance Learning
DOI: 10.5517/cc11rz81
title: CCDC 976353: Experimental Crystal Structure Determination

description: Related Article: Daniel J. Meininger,  Jonathan D. Caranto,  Hadi D. Arman,  and Zachary J. Tonzetich|2013|Inorg.Chem.|52|12468|doi:10.1021/ic401467k
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/cc11rz92
title: CCDC 976354: Experimental Crystal Structure Determination

description: Related Article: Daniel J. Meininger,  Jonathan D. Caranto,  Hadi D. Arman,  and Zachary J. Tonzetich|2013|Inorg.Chem.|52|12468|doi:10.1021/ic401467k
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/cc105rqn
title: CCDC 929061: Experimental Crystal Structure Determination

description: Related Article: Zulema Arcís-Castillo,  Francisco J. Muñoz-Lara,  M. Carmen Muñoz,  Daniel Aravena,  Ana B. Gaspar,  Juan F. Sánchez-Royo,  Eliseo Ruiz,  Masaaki Ohba,  Ryotaro Matsuda,  Susumu Kitagawa,  and José A. Real|2013|Inorg.Chem.|52|12777|doi:10.1021/ic4020477
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.cc11rzrj
title: CCDC 976368: Experimental Crystal Structure Determination

description: Related Article: Dragoslav Ilić, Verica V. Jevtić, Miorad M. Vasojević, Miodrag Ž. Jelić, Ivana D. Radojević, Ljiljana R. Čomić, Slađana B. Novaković, Goran A. Bogdanović, Ivan Potočňák, Srećko R. Trifunović|2015|Polyhedron|85|1|doi:10.1016/j.poly.2014.08.013
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/cc11s04z
title: CCDC 976380: Experimental Crystal Structure Determination

description: Related Article: A.S. Al-Fahdawi, H.A. Al-Kafajy, M.J. Al-Jeboori, S.J. Coles, C. Wilson, H. Potgieter|2014|Acta Crystallogr.,Sect.E:Struct.Rep.Online|70|o66|doi:10.1107/S1600536813033497
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/cc11s072
title: CCDC 976383: Experimental Crystal Structure Determination

description: Related Article: Lankani P. Wijesinghe, Buddhie S. Lankage, Gearóid M. Ó Máille, Sarath D. Perera, Deanne Nolan, Longsheng Wang, Sylvia M. Draper|2014|Chem.Commun.|50|10637|doi:10.1039/C4CC03577A
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.cc11s083
title: CCDC 976384: Experimental Crystal Structure Determination

description: Related Article: Guilherme A. M. Jardim,  Eduardo H. G. Cruz,  Wagner O. Valença, Jarbas M. Resende,  Bernardo L. Rodrigues,  Daniela F. Ramos,  Ronaldo N. Oliveira, Pedro E. A. Silva and Eufrânio N. da Silva Júnior|2015|J.Braz.Chem.Soc.|26|1013|doi:10.5935/0103-5053.20150067
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: 10.13140/rg.2.2.29611.96804
title: Data. Water Sports
DOI: 10.5517/ccdc.csd.cc11s094
title: CCDC 976385: Experimental Crystal Structure Determination

description: Related Article: Guilherme A. M. Jardim,  Eduardo H. G. Cruz,  Wagner O. Valença, Jarbas M. Resende,  Bernardo L. Rodrigues,  Daniela F. Ramos,  Ronaldo N. Oliveira, Pedro E. A. Silva and Eufrânio N. da Silva Júnior|2015|J.Braz.Chem.Soc.|26|1013|doi:10.5935/0103-5053.20150067
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/cc11s0g9
title: CCDC 976390: Experimental Crystal Structure Determination

description: Related Article: Paulo N. Martinho, Ana I. Vicente, Sara Realista, Marta S. Saraiva, Ana I. Melato, Paula Brandão, Liliana P. Ferreira, Maria de Deus Carvalho|2014|J.Organomet.Chem.|760|48|doi:10.1016/j.jorganchem.2013.12.028
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/cc11s0sm
title: CCDC 976400: Experimental Crystal Structure Determination

description: Related Article: G. Smith|2014|Acta Crystallogr.,Sect.E:Struct.Rep.Online|70|m23|doi:10.1107/S1600536813033503
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/cc11s0tn
title: CCDC 976401: Experimental Crystal Structure Determination

description: Related Article: Hanan I. Althagbi, Alison J. Edwards, Brian K. Nicholson, Daniel A. Reason, Graham C. Saunders, Sophie A. Sim, Danielle A. van der Heijden|2016|Cryst.Growth Des.|16|174|doi:10.1021/acs.cgd.5b01077
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/cc11s0wq
title: CCDC 976403: Experimental Crystal Structure Determination

description: Related Article: C.Xu, G.Tian, S.J.Teat, G.Liu, L.Rao|2013|Chem.-Eur.J.|19|16690|doi:10.1002/chem.201302119
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/cc11s0xr
title: CCDC 976404: Experimental Crystal Structure Determination

description: Related Article: C.Xu, G.Tian, S.J.Teat, G.Liu, L.Rao|2013|Chem.-Eur.J.|19|16690|doi:10.1002/chem.201302119
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.