cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5066/p974vcdk
title: Southwestern Riparian Plant Trait Matrix, Colorado River, Grand Canyon, Arizona (ver. 2.0, 2022)

description: Trait-based approaches to vegetation analyses are becoming more prevalent in studies of riparian vegetation dynamics, including responses to flow regulation, groundwater pumping, and climate change. These analyses require species trait data compiled from the literature and floras or original field measurements. Gathering such data makes trait-based research time intensive at best and impracticable in some cases. To support trait-based analysis of vegetation along the Colorado River through Grand Canyon, a data set of 20 biological traits and ecological affinities for 179 species occurring in that study area was compiled. This diverse flora shares species with many riparian areas in the western USA and includes species that occur across a wide moisture gradient. This dataset contains information on the physical traits and environmental tolerances of plant species occurring along the lower Colorado River through Grand Canyon. Due to the unique combination of plant species within the Grand Canyon, this flora shares species with many riparian areas in the western U.S.A. and represents obligate wetland to obligate upland plant species. Data were compiled from published scientific papers, unpublished reports, plant fact sheets, existing trait databases, regional floras, and plant guides. Data for ordinal environmental tolerances were more readily available than were quantitative traits. Categorical, ordinal, and continuous data are included in this dataset. Also, this dataset includes data from McCoy-Sulentic et al. 2017, who measured or compiled data on specific leaf area (SLA), stem specific gravity (SSG), seed mass, and mature height of 110 plant species that occur along the Colorado River in Grand Canyon, Arizona. Additionally, they measured leaf &amp;delta;13C, &amp;delta;15N, % carbon, % nitrogen, and C/N ratio of 56 species with C3 photosynthesis. This dataset does not contain sensitive or classified data.
DOI: 10.5281/zenodo.5914195
title: MetaCOXI: An integrated collection of metazoan cytochrome oxidase subunit-I DNA sequences

description: <strong>MetaCOXI Sequences in fasta format</strong> This collection is based on the integration of the European Nucleotide Archive (ENA, release 142) and the Barcode of Life Data Systems (BOLD: http://www.boldsystems.org/) data. <strong>CONTENT: </strong>Currently it contains 5,608,848 entries of metazoan COXI sequences and their corresponding taxonomic classification and metadata. MetaCOXI_Seqs.tar.gz contains the full sequence collection in 'fasta' format. MetaCOXI_Taxonomy_Metadata.tar.gz contains the entries-associated taxonomy path and additional metadata Taxonomic path are provided for the following seven levels with their NCBI-TaxIDs: Kingdom, Phylum, Class, Order, Family, Genus, Species. For additional information visit: https://github.com/bachob5/MetaCOXI
DOI: 10.5281/zenodo.5930274
title: Replication Package for: Welfare and Redistribution in Residential Electricity Markets with Solar Power

description: The Stata Do-Files, Matlab Scripts and Functions in this folder can be used to replicate the tables and graphs of the paper "Welfare and Redistribution in Residential Electricity Markets with Solar Power" by Fabian Feger, Nicola Pavanini, and Doina Radulescu.
DOI: 10.5281/zenodo.5560867
title: Replication Package for: Welfare and Redistribution in Residential Electricity Markets with Solar Power

description: The Stata Do-Files, Matlab Scripts and Functions in this folder can be used to replicate the tables and graphs of the paper "Welfare and Redistribution in Residential Electricity Markets with Solar Power" by Fabian Feger, Nicola Pavanini, and Doina Radulescu.
DOI: 10.6073/pasta/dd06df3f950afe4a4642306182237d13
title: Long-term study of tree cholla demography in the Los Pinos mountains, Sevilleta National Wildlife Refuge

description: This study was initiated in 2004 by TEX Miller to quantify individual-level demographic rates of tree cholla cacti (Cylindriopuntia imbricata) at the Sevilleta National Wildlife Refuge, Socorro Co., NM. This data package spans 2004-2018, though the study is maintained through the present. In each year, censuses were conducted over several days in the last week of May and/or the first week of June. Individuals were marked with aluminum tags and tracked longitudinally through time, with annual measures of survival, size, reproductive output, and interactions with insect herbivores and mutualists (extra-floral nectar-feeding ants). For the years 2004-2008, plants were grouped into spatial blocks (T1, T2, T3) lacking defined boundaries. Beginning in 2009, the study design changed to 30m x 30m plots (Plots 1-8) with an entirely new cohort of individuals that does not overlap with the 2004-2008 data. From 2009 onward, plots were searched each year and new plants were added to the census as they were discovered. Seedlings typically require several years of growth before they are detectable in our census, so counts of new plants in a given year do not necessarily reflect recruitment in that year. The data frame is set up such that one row is a transition year (May of year t to May of year t+1) for one individual; this means that all but the first and last years’ observations occur twice, once as the start of a transition year and once as the end.
DOI: 10.5519/qd.aup0z89e
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (1386 records)
DOI: 10.23634/mmudr.00629087
title: Lateral force removal of fungal spores to demonstrate how surface properties affect fungal spore retention

description: Microbial biofouling on polymer surfaces can lead to their biodeterioration. This may result in deterioration of the surface leading to cracking and fracturing. Fungal spores from Aspergillus niger 1957, Aspergillus niger 1988 and Aureobasidium pullulans were tested to determine their strength of attachment on three surfaces, p(γ-MPS-co-MMA), p(γ-MPS-co-LMA), and spin coated PMMA (PMMAsc) using lateral force measurements. The results demonstrated that A. niger 1957 and A. niger 1988 spores were most easily removed from the p(γ-MPS-co-MMA) surface, which was the surface with the highest Ra value. The A. niger 1957 and A. pullulans spores were most difficult to remove from the PMMAsc surface which was the hardest surface. A. niger 1988 spores were the most difficult to remove from p(γ-MPS-co-LMA), the most hydrophobic surface. The results with A. pullulans were difficult to elucidate since the spores bound to all three surfaces and were removed with similar rates of force. The lateral force results demonstrated that spore attachment to a surface is a multifactorial process, and independent surface and microbial factors influence spore binding. Thus, each environmental scenario needs to be considered on an individual basis, since a solution to one biofouling issue will probably not translate across to other systems.
DOI: 10.17036/researchdata.aston.ac.uk.00000536
title: Mode division multiplexing free space optical transmission
DOI: 10.5281/zenodo.5906262
title: Sampled ΔH/Δλ and ΔH data from ABFE calculations of 12 ligands bound to PWWP1

description: Supplementary Information: "Evaluating the use of absolute binding free energy in the fragment optimization process" Included are the ABFE raw free energy samples for multiple replicates (labelled by `run` number) of 12 ligands to bound PWWP1. These ligands are originally detailed by Böttcher et al. (https://doi.org/10.1038/s41589-019-0310-x). All samples are provided as a set of `.xvg` files as generated by GROMACS 2021 (https://doi.org/10.5281/zenodo.5849961). The `.xvg` files are labelled as dhdl.N.xvg where N represents the λ state the free energy values were sampled from. The `.xvg` files contain both ΔH/Δλ and ΔH values, please see the header of each files for more information. Samples detailing the partial decoupling of the ligand from the protein-ligand complex are contained within the `complex` folder. These consist of an orientational restraint addition step (found within the `restraints-xvg` folders), charge annihilation step (found within the `coul-xvg` folders), and Van der Waals decoupling step (found within the `vdw-xvg` folders). Samples detailing the partial decoupling of the ligand from solvent are contained within the `ligand` folder and consist of a charge annihilation step (found within the individual `coul-xvg` folders) and a Van der Waals decoupling step (found within the individual `vdw-xvg` folders).
DOI: 10.5281/zenodo.5906261
title: Sampled ΔH/Δλ and ΔH data from ABFE calculations of 12 ligands bound to PWWP1

description: Supplementary Information: "Evaluating the use of absolute binding free energy in the fragment optimization process" Included are the ABFE raw free energy samples for multiple replicates (labelled by `run` number) of 12 ligands to bound PWWP1. These ligands are originally detailed by Böttcher et al. (https://doi.org/10.1038/s41589-019-0310-x). All samples are provided as a set of `.xvg` files as generated by GROMACS 2021 (https://doi.org/10.5281/zenodo.5849961). The `.xvg` files are labelled as dhdl.N.xvg where N represents the λ state the free energy values were sampled from. The `.xvg` files contain both ΔH/Δλ and ΔH values, please see the header of each files for more information. Samples detailing the partial decoupling of the ligand from the protein-ligand complex are contained within the `complex` folder. These consist of an orientational restraint addition step (found within the `restraints-xvg` folders), charge annihilation step (found within the `coul-xvg` folders), and Van der Waals decoupling step (found within the `vdw-xvg` folders). Samples detailing the partial decoupling of the ligand from solvent are contained within the `ligand` folder and consist of a charge annihilation step (found within the individual `coul-xvg` folders) and a Van der Waals decoupling step (found within the individual `vdw-xvg` folders).
DOI: 10.5281/zenodo.5906110
title: Sampled ΔH/Δλ and ΔH data from ABFE calculations of 18 ligands bound to HSP90

description: Supplementary Information: "Evaluating the use of absolute binding free energy in the fragment optimization process" Included are the ABFE raw free energy samples for multiple replicates (labelled by `run` number) of 18 ligands bound to HSP90. These ligands are originally detailed by Murray et al. (https://doi.org/10.1021/jm100059d). All samples are provided as a set of `.xvg` files as generated by GROMACS 2021 (https://doi.org/10.5281/zenodo.5849961). The `.xvg` files are labelled as dhdl.N.xvg where N represents the λ state the free energy values were sampled from. The `.xvg` files contain both ΔH/Δλ and ΔH values, please see the header of each files for more information. Samples detailing the partial decoupling of the ligand from the protein-ligand complex are contained within the `complex` folder. These consist of an orientational restraint addition step (found within the `restraints-xvg` folders), charge annihilation step (found within the `coul-xvg` folders), and Van der Waals decoupling step (found within the `vdw-xvg` folders). Samples detailing the partial decoupling of the ligand from solvent are contained within the `ligand` folder and consist of a charge annihilation step (found within the individual `coul-xvg` folders) and a Van der Waals decoupling step (found within the individual `vdw-xvg` folders).
DOI: 10.5281/zenodo.5906109
title: Sampled ΔH/Δλ and ΔH data from ABFE calculations of 18 ligands bound to HSP90

description: Supplementary Information: "Evaluating the use of absolute binding free energy in the fragment optimization process" Included are the ABFE raw free energy samples for multiple replicates (labelled by `run` number) of 18 ligands bound to HSP90. These ligands are originally detailed by Murray et al. (https://doi.org/10.1021/jm100059d). All samples are provided as a set of `.xvg` files as generated by GROMACS 2021 (https://doi.org/10.5281/zenodo.5849961). The `.xvg` files are labelled as dhdl.N.xvg where N represents the λ state the free energy values were sampled from. The `.xvg` files contain both ΔH/Δλ and ΔH values, please see the header of each files for more information. Samples detailing the partial decoupling of the ligand from the protein-ligand complex are contained within the `complex` folder. These consist of an orientational restraint addition step (found within the `restraints-xvg` folders), charge annihilation step (found within the `coul-xvg` folders), and Van der Waals decoupling step (found within the `vdw-xvg` folders). Samples detailing the partial decoupling of the ligand from solvent are contained within the `ligand` folder and consist of a charge annihilation step (found within the individual `coul-xvg` folders) and a Van der Waals decoupling step (found within the individual `vdw-xvg` folders).
DOI: 10.5281/zenodo.5904110
title: Sampled ΔH/Δλ and ΔH data from ABFE calculations of 10 ligands bound to Cyclophilin D

description: Supplementary Information: "Evaluating the use of absolute binding free energy in the fragment optimization process" Included are the ABFE raw free energy samples for multiple replicates (labelled by `run` number) of 10 ligands bound to Cyclophilin D. These ligands are originally detailed by Grädler et al. (https://doi.org/10.1016/j.bmcl.2019.126717). Unlike the other Cyclophilin D<br> dataset provided in this work, simulations for these ABFE calculations were carried out using hydrogen mass repartitioning (HMR). The MCL-1, HSP90, and PWWP1 also used HMR. All samples are provided as a set of `.xvg` files as generated by GROMACS 2021 (https://doi.org/10.5281/zenodo.5849961). The `.xvg` files are labelled as dhdl.N.xvg where N represents the λ state the free energy values were sampled from. The `.xvg` files contain both ΔH/Δλ and ΔH values, please see the header of each files for more information. Samples detailing the partial decoupling of the ligand from the protein-ligand complex are contained within the `complex` folder. These consist of an orientational restraint addition step (found within the `restraints-xvg` folders), charge annihilation step (found within the `coul-xvg` folders), and Van der Waals decoupling step (found within the `vdw-xvg` folders). Samples detailing the partial decoupling of the ligand from solvent are contained within the `ligand` folder and consist of a charge annihilation step (found within the individual `coul-xvg` folders) and a Van der Waals decoupling step (found within the individual `vdw-xvg` folders).<br>
DOI: 10.5281/zenodo.5904109
title: Sampled ΔH/Δλ and ΔH data from ABFE calculations of 10 ligands bound to Cyclophilin D

description: Supplementary Information: "Evaluating the use of absolute binding free energy in the fragment optimization process" Included are the ABFE raw free energy samples for multiple replicates (labelled by `run` number) of 10 ligands bound to Cyclophilin D. These ligands are originally detailed by Grädler et al. (https://doi.org/10.1016/j.bmcl.2019.126717). Unlike the other Cyclophilin D<br> dataset provided in this work, simulations for these ABFE calculations were carried out using hydrogen mass repartitioning (HMR). The MCL-1, HSP90, and PWWP1 also used HMR. All samples are provided as a set of `.xvg` files as generated by GROMACS 2021 (https://doi.org/10.5281/zenodo.5849961). The `.xvg` files are labelled as dhdl.N.xvg where N represents the λ state the free energy values were sampled from. The `.xvg` files contain both ΔH/Δλ and ΔH values, please see the header of each files for more information. Samples detailing the partial decoupling of the ligand from the protein-ligand complex are contained within the `complex` folder. These consist of an orientational restraint addition step (found within the `restraints-xvg` folders), charge annihilation step (found within the `coul-xvg` folders), and Van der Waals decoupling step (found within the `vdw-xvg` folders). Samples detailing the partial decoupling of the ligand from solvent are contained within the `ligand` folder and consist of a charge annihilation step (found within the individual `coul-xvg` folders) and a Van der Waals decoupling step (found within the individual `vdw-xvg` folders).<br>
DOI: 10.5281/zenodo.5906019
title: Sampled ΔH/Δλ and ΔH data from ABFE calculations (using standard atomic masses) of 10 ligands bound to Cyclophilin D

description: Supplementary Information: "Evaluating the use of absolute binding free energy in the fragment optimization process" Included are the ABFE raw free energy samples for multiple replicates (labelled by `run` number) of 10 ligands to bound Cyclophilin D. These ligands are originally detailed by Grädler et al. (https://doi.org/10.1016/j.bmcl.2019.126717). Unlike other datasets in this work, which employed hydrogen mass repartitioning, the ligands here were calculated using standard atomic masses. All samples are provided as a set of `.xvg` files as generated by GROMACS 2021 (https://doi.org/10.5281/zenodo.5849961). The `.xvg` files are labelled as dhdl.N.xvg where N represents the λ state the free energy values were sampled from. The `.xvg` files contain both ΔH/Δλ and ΔH values, please see the header of each files for more information. Samples detailing the partial decoupling of the ligand from the protein-ligand complex are contained within the `complex` folder. These consist of an orientational restraint addition step (found within the `restraints-xvg` folders), charge annihilation step (found within the `coul-xvg` folders), and Van der Waals decoupling step (found within the `vdw-xvg` folders). Samples detailing the partial decoupling of the ligand from solvent are contained within the `ligand` folder and consist of a charge annihilation step (found within the individual `coul-xvg` folders) and a Van der Waals decoupling step (found within the individual `vdw-xvg` folders).
DOI: 10.5281/zenodo.5906018
title: Sampled ΔH/Δλ and ΔH data from ABFE calculations (using standard atomic masses) of 10 ligands bound to Cyclophilin D

description: Supplementary Information: "Evaluating the use of absolute binding free energy in the fragment optimization process" Included are the ABFE raw free energy samples for multiple replicates (labelled by `run` number) of 10 ligands to bound Cyclophilin D. These ligands are originally detailed by Grädler et al. (https://doi.org/10.1016/j.bmcl.2019.126717). Unlike other datasets in this work, which employed hydrogen mass repartitioning, the ligands here were calculated using standard atomic masses. All samples are provided as a set of `.xvg` files as generated by GROMACS 2021 (https://doi.org/10.5281/zenodo.5849961). The `.xvg` files are labelled as dhdl.N.xvg where N represents the λ state the free energy values were sampled from. The `.xvg` files contain both ΔH/Δλ and ΔH values, please see the header of each files for more information. Samples detailing the partial decoupling of the ligand from the protein-ligand complex are contained within the `complex` folder. These consist of an orientational restraint addition step (found within the `restraints-xvg` folders), charge annihilation step (found within the `coul-xvg` folders), and Van der Waals decoupling step (found within the `vdw-xvg` folders). Samples detailing the partial decoupling of the ligand from solvent are contained within the `ligand` folder and consist of a charge annihilation step (found within the individual `coul-xvg` folders) and a Van der Waals decoupling step (found within the individual `vdw-xvg` folders).
DOI: 10.5281/zenodo.5906805
title: Sampled ΔH/Δλ and ΔH data from ABFE calculations of 19 ligands bound to MCL-1

description: Supplementary Information: "Evaluating the use of absolute binding free energy in the fragment optimization process" Included are the ABFE raw free energy samples for multiple replicates (labelled by `run` number) of 19 ligands to bound MCL-1. These ligands are originally detailed by Friberg et al. (https://doi.org/10.1021/jm301448p). All samples are provided as a set of `.xvg` files as generated by GROMACS 2021 (https://doi.org/10.5281/zenodo.5849961). The `.xvg` files are labelled as dhdl.N.xvg where N represents the λ state the free energy values were sampled from. The `.xvg` files contain both ΔH/Δλ and ΔH values, please see the header of each files for more information. Samples detailing the partial decoupling of the ligand from the protein-ligand complex are contained within the `complex` folder. These consist of an orientational restraint addition step (found within the `restraints-xvg` folders), charge annihilation step (found within the `coul-xvg` folders), and Van der Waals decoupling step (found within the `vdw-xvg` folders). Samples detailing the partial decoupling of the ligand from solvent are contained within the `ligand` folder and consist of a charge annihilation step (found within the individual `coul-xvg` folders) and a Van der Waals decoupling step (found within the individual `vdw-xvg` folders).
DOI: 10.5281/zenodo.5906804
title: Sampled ΔH/Δλ and ΔH data from ABFE calculations of 19 ligands bound to MCL-1

description: Supplementary Information: "Evaluating the use of absolute binding free energy in the fragment optimization process" Included are the ABFE raw free energy samples for multiple replicates (labelled by `run` number) of 19 ligands to bound MCL-1. These ligands are originally detailed by Friberg et al. (https://doi.org/10.1021/jm301448p). All samples are provided as a set of `.xvg` files as generated by GROMACS 2021 (https://doi.org/10.5281/zenodo.5849961). The `.xvg` files are labelled as dhdl.N.xvg where N represents the λ state the free energy values were sampled from. The `.xvg` files contain both ΔH/Δλ and ΔH values, please see the header of each files for more information. Samples detailing the partial decoupling of the ligand from the protein-ligand complex are contained within the `complex` folder. These consist of an orientational restraint addition step (found within the `restraints-xvg` folders), charge annihilation step (found within the `coul-xvg` folders), and Van der Waals decoupling step (found within the `vdw-xvg` folders). Samples detailing the partial decoupling of the ligand from solvent are contained within the `ligand` folder and consist of a charge annihilation step (found within the individual `coul-xvg` folders) and a Van der Waals decoupling step (found within the individual `vdw-xvg` folders).
DOI: 10.5281/zenodo.5913469
title: Benchmark set inputs for absolute binding free energy calculations of fragment optimisations

description: Supplementary Information: "Evaluating the use of absolute binding free energy in the fragment optimization process" Provided here are the various scripts, input files, and results necessary to reproduce the outcomes of the above mentioned publication. Please see the provided README.md files for further information on the contents of this dataset.
DOI: 10.5281/zenodo.5913468
title: Benchmark set inputs for absolute binding free energy calculations of fragment optimisations

description: Supplementary Information: "Evaluating the use of absolute binding free energy in the fragment optimization process" Provided here are the various scripts, input files, and results necessary to reproduce the outcomes of the above mentioned publication. Please see the provided README.md files for further information on the contents of this dataset.