cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.13084199
title: Molecular recognition of acetylcholinesterase and its subnanomolar reversible inhibitor: a molecular simulations study

description: Recently, we designed and synthesized a subnanomolar, reversible, dual-binding site acetylcholinesterase (AChE) inhibitor which consists of the tacrine and aroylacrylic acid phenylamide moieties, mutually linked by eight methylene units. To further investigate the process of the molecular recognition between the AChE and its inhibitor, we performed six unconstrained molecular dynamics (MD) simulations, where the compound in three possible protonation states was placed inside binding sites of two available AChE crystal structures. In all six MD trajectories, the ligand generally occupied similar space inside the AChE active site, but the pattern of the interactions between the ligand functional groups and the amino acid residues was significantly different and highly dependent upon the crystal structure used to generate initial systems for simulation. The greatest differences were observed between the trajectories obtained with different AChE crystal structures used as starting target conformations. In some trajectories, several unusual positions and dynamic behavior of the tacrine moiety were observed. Therefore, this study provides important structure-based data useful in further optimization of the reversible, dual binding AChE inhibitors, and also emphasizes the importance of the starting crystal structure used for dynamics as well as the protonation state of the reversible inhibitors. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.13084199.v1
title: Molecular recognition of acetylcholinesterase and its subnanomolar reversible inhibitor: a molecular simulations study

description: Recently, we designed and synthesized a subnanomolar, reversible, dual-binding site acetylcholinesterase (AChE) inhibitor which consists of the tacrine and aroylacrylic acid phenylamide moieties, mutually linked by eight methylene units. To further investigate the process of the molecular recognition between the AChE and its inhibitor, we performed six unconstrained molecular dynamics (MD) simulations, where the compound in three possible protonation states was placed inside binding sites of two available AChE crystal structures. In all six MD trajectories, the ligand generally occupied similar space inside the AChE active site, but the pattern of the interactions between the ligand functional groups and the amino acid residues was significantly different and highly dependent upon the crystal structure used to generate initial systems for simulation. The greatest differences were observed between the trajectories obtained with different AChE crystal structures used as starting target conformations. In some trajectories, several unusual positions and dynamic behavior of the tacrine moiety were observed. Therefore, this study provides important structure-based data useful in further optimization of the reversible, dual binding AChE inhibitors, and also emphasizes the importance of the starting crystal structure used for dynamics as well as the protonation state of the reversible inhibitors. Communicated by Ramaswamy H. Sarma
DOI: 10.25345/c51c1tg3n
title: MassIVE Reanalysis RMSV000000354.3114 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, PRSS33 [launched by fce971e5ede541cca3fc5307a73294d8]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c5wp9t70z
title: MassIVE Reanalysis RMSV000000354.3112 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, BUB1 [launched by fce971e5ede541cca3fc5307a73294d8]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c5rx93d72
title: MassIVE Reanalysis RMSV000000354.3115 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, SNX1 [launched by fce971e5ede541cca3fc5307a73294d8]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c5n58cm4q
title: MassIVE Reanalysis RMSV000000354.3051 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, ACOT11 [launched by fce971e5ede541cca3fc5307a73294d8]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c5hd7nt0k
title: MassIVE Reanalysis RMSV000000354.3117 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, RG9MTD1 [launched by fce971e5ede541cca3fc5307a73294d8]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c5cn6z05r
title: MassIVE Reanalysis RMSV000000354.3116 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, ADIPOR2 [launched by fce971e5ede541cca3fc5307a73294d8]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c57w67610
title: MassIVE Reanalysis RMSV000000354.3120 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, ASTN2 [launched by fce971e5ede541cca3fc5307a73294d8]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c5445hc81
title: MassIVE Reanalysis RMSV000000354.3083 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, GPRC5C [launched by fce971e5ede541cca3fc5307a73294d8]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.6084/m9.figshare.19205148
title: Data for "Compositional Trends in Surface Enhanced Diffusion in Lead Silicate Glasses"

description: Supporting information for the paper:<br>Compositional Trends in Surface Enhanced Diffusion in Lead Silicate Glasses, by A. Annamareddy, M. Molina-Ruiz, D. Horton-Bailey, F. Hellman, Y. Li, L. Yu, and D. Morgan, Submitted to Computational Materials Science (2022).<br>Please see paper and README file here for more information.<br>
DOI: 10.6084/m9.figshare.19205148.v1
title: Data for "Compositional Trends in Surface Enhanced Diffusion in Lead Silicate Glasses"

description: Supporting information for the paper:<br>Compositional Trends in Surface Enhanced Diffusion in Lead Silicate Glasses, by A. Annamareddy, M. Molina-Ruiz, D. Horton-Bailey, F. Hellman, Y. Li, L. Yu, and D. Morgan, Submitted to Computational Materials Science (2022).<br>Please see paper and README file here for more information.<br>
DOI: 10.25345/c50g3gz57
title: MassIVE Reanalysis RMSV000000354.3119 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, GYPB [launched by fce971e5ede541cca3fc5307a73294d8]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c5vq2sb1r
title: MassIVE Reanalysis RMSV000000354.3118 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, DUSP6 [launched by fce971e5ede541cca3fc5307a73294d8]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c5qz22h8v
title: MassIVE Reanalysis RMSV000000354.3121 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, AEBP2 [launched by fce971e5ede541cca3fc5307a73294d8]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c5m61bq41
title: MassIVE Reanalysis RMSV000000354.3123 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, HLA-B [launched by fce971e5ede541cca3fc5307a73294d8]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c5gf0mw9s
title: MassIVE Reanalysis RMSV000000354.3124 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, GDF10 [launched by fce971e5ede541cca3fc5307a73294d8]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c5bn9x35h
title: MassIVE Reanalysis RMSV000000354.3125 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, ZDHHC20 [launched by fce971e5ede541cca3fc5307a73294d8]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c56w96927
title: MassIVE Reanalysis RMSV000000354.3122 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, KATNB1 [launched by fce971e5ede541cca3fc5307a73294d8]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c53775v94
title: MassIVE Reanalysis RMSV000000354.3127 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, RHCG [launched by fce971e5ede541cca3fc5307a73294d8]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.48370/ofd/qxmg4d/z55nln
title: Microbotryum saponariae Lutz, Göker, Piątek, Kemler, Begerow & Oberwinkler F-2534.tif

description: :unav
DOI: 10.48370/ofd/qxmg4d
title: Microbotryum saponariae Lutz, Göker, Piątek, Kemler, Begerow Oberwinkler, 2534

description: Fungarium Micromycetes
DOI: 10.48370/ofd/b8z6fn/0ywway
title: Microbotryum stellariae (Sowerby) Deml & Oberwinkler F-4284.tif

description: :unav
DOI: 10.48370/ofd/b8z6fn
title: Microbotryum stellariae (Sowerby) Deml Oberwinkler, 4284

description: Fungarium Micromycetes
DOI: 10.48370/ofd/tqmpb1/r54cdd
title: Microbotryum stellariae (Sowerby) Deml & Oberwinkler F-3988.tif

description: :unav
DOI: 10.48370/ofd/tqmpb1
title: Microbotryum stellariae (Sowerby) Deml Oberwinkler, 3988

description: Fungarium Micromycetes
DOI: 10.25345/c5zg6g75n
title: MassIVE Reanalysis RMSV000000354.3126 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, RPS8 [launched by fce971e5ede541cca3fc5307a73294d8]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.48370/ofd/th64jm/scuj9u
title: Microbotryum stellariae (Sowerby) Deml & Oberwinkler F-2157.tif

description: :unav
DOI: 10.48370/ofd/th64jm
title: Microbotryum stellariae (Sowerby) Deml Oberwinkler, 2157

description: Fungarium Micromycetes
DOI: 10.48370/ofd/dhw01d/cerrrr
title: Microbotryum stellariae (Sowerby) Deml & Oberwinkler F-1279 (2).tif

description: :unav
DOI: 10.48370/ofd/2oewtm/6wlk1z
title: Microbotryum stellariae (Sowerby) Deml & Oberwinkler F-0772.tif

description: :unav
DOI: 10.5281/zenodo.6115404
title: QuerTCI: A Tool Integrating GitHub Issue Querying with Comment Classification

description: Issue tracking systems enable users and developers to comment on problems plaguing a software system. Empirical Software Engineering (ESE) researchers study (open-source) project issues and the comments and threads within to discover---among others---challenges developers face when, e.g., incorporating new technologies, platforms, and programming language constructs. However, issue discussion threads accumulate over time and thus can become unwieldy, hindering any insight that researchers may gain. While existing approaches alleviate this burden by classifying issue thread comments, there is a gap between searching popular open-source software repositories (e.g., those on GitHub) for issues containing particular keywords and feeding the results into a classification model. In this paper, we demonstrate a research infrastructure tool called QuerTCI that bridges this gap by integrating the GitHub issue comment search API with the classification models found in existing approaches. Using queries, ESE researchers can retrieve GitHub issues containing particular keywords, e.g., those related to a certain programming language construct, and subsequently classify the kinds of discussions occurring in those issues. Using our tool, our hope is that ESE researchers can uncover challenges related to particular technologies using certain keywords through popular open-source repositories more seamlessly than previously possible. A tool demonstration video may be found at: https://youtu.be/fADKSxn0QUk.
DOI: 10.48370/ofd/2oewtm
title: Microbotryum stellariae (Sowerby) Deml Oberwinkler, 772

description: Fungarium Micromycetes
DOI: 10.48370/ofd/dhw01d/k9hich
title: Microbotryum stellariae (Sowerby) Deml & Oberwinkler F-1279.tif

description: :unav
DOI: 10.5281/zenodo.6115403
title: QuerTCI: A Tool Integrating GitHub Issue Querying with Comment Classification

description: Issue tracking systems enable users and developers to comment on problems plaguing a software system. Empirical Software Engineering (ESE) researchers study (open-source) project issues and the comments and threads within to discover---among others---challenges developers face when, e.g., incorporating new technologies, platforms, and programming language constructs. However, issue discussion threads accumulate over time and thus can become unwieldy, hindering any insight that researchers may gain. While existing approaches alleviate this burden by classifying issue thread comments, there is a gap between searching popular open-source software repositories (e.g., those on GitHub) for issues containing particular keywords and feeding the results into a classification model. In this paper, we demonstrate a research infrastructure tool called QuerTCI that bridges this gap by integrating the GitHub issue comment search API with the classification models found in existing approaches. Using queries, ESE researchers can retrieve GitHub issues containing particular keywords, e.g., those related to a certain programming language construct, and subsequently classify the kinds of discussions occurring in those issues. Using our tool, our hope is that ESE researchers can uncover challenges related to particular technologies using certain keywords through popular open-source repositories more seamlessly than previously possible. A tool demonstration video may be found at: https://youtu.be/fADKSxn0QUk.
DOI: 10.48370/ofd/dhw01d/3e0vc1
title: Microbotryum stellariae (Sowerby) Deml & Oberwinkler F-1279 (4).tif

description: :unav
DOI: 10.48370/ofd/dhw01d/altxqf
title: Microbotryum stellariae (Sowerby) Deml & Oberwinkler F-1279 (3).tif

description: :unav
DOI: 10.48370/ofd/zxflxq/o3vsom
title: Microbotryum stellariae (Sowerby) Deml & Oberwinkler F-4212 (4).tif

description: :unav
DOI: 10.48370/ofd/dhw01d/m62vue
title: Microbotryum stellariae (Sowerby) Deml & Oberwinkler F-1279.jpg

description: :unav
DOI: 10.48370/ofd/zxflxq/eeavll
title: Microbotryum stellariae (Sowerby) Deml & Oberwinkler F-4212.tif

description: :unav
DOI: 10.48370/ofd/dhw01d/5ffbkt
title: Microbotryum stellariae (Sowerby) Deml & Oberwinkler F-1279 (5).tif

description: :unav
DOI: 10.48370/ofd/dhw01d
title: Microbotryum stellariae (Sowerby) Deml Oberwinkler, 1279

description: Fungarium Micromycetes
DOI: 10.48370/ofd/zxflxq/el4oku
title: Microbotryum stellariae (Sowerby) Deml & Oberwinkler F-4212 (2).tif

description: :unav
DOI: 10.48370/ofd/ydhfkd/kfyekh
title: Microbotryum stellariae (Sowerby) Deml & Oberwinkler F-2562.tif

description: :unav
DOI: 10.48370/ofd/zxflxq/xn6vfn
title: Microbotryum stellariae (Sowerby) Deml & Oberwinkler F-4212 (3).tif

description: :unav
DOI: 10.48370/ofd/zxflxq
title: Microbotryum stellariae (Sowerby) Deml Oberwinkler, 4212

description: Fungarium Micromycetes
DOI: 10.48370/ofd/ydhfkd
title: Microbotryum stellariae (Sowerby) Deml Oberwinkler, 2562

description: Fungarium Micromycetes