cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.10500769
title: Water will find its way: transport through narrow tunnels in hydrolases (Epx protein)

description: Water will find its way: transport through narrow tunnels in hydrolases (Epx protein)

The input files and results used for the paper “Water will find its way: transport through narrow tunnels in hydrolases” are separated in the different folders depending the stage they belong to.



01_Simulations.tar.gz: All the files used to get the data employing Molecular Dynamics simulations.

02_Caver.tar.gz: Caver config used together with the Divide-and-conquer approach to study protein tunnels in long molecular dynamics simulations method (https://doi.org/10.1016/j.mex.2022.101968), and after re-clustering as described in the methods section of the paper.

03_Aquaduct.tar.gz: Aquaduct results for all the MD trajectories.

04_TransportTools.tar.gz: TransportTools results (https://doi.org/10.1093/bioinformatics/btab872).

05_WaterAnalysis.tar.gz: The results from the exact matching analysis were parsed to perform H-bond analysis. Here are the PDBs where the minimum sphere event is present. Also the txt files with the results from the H-bond and contact analyses are here.


Files



01_build_database.py Python3 script to parse the results from the exact matching analysis from TransportTools into a dictionary of transport events. For more detailed information read the script documentation.

Epx.dat Parsed database of transport events for Epx system. Command used: python3 01_build_database.py -c 04_TransportTools/Epx_tt.ini -o Epx.dat
description: This work was supported by the National Science Centre, Poland (grant no. 2017/26/E/NZ1/00548). The computations were performed at the Poznan Supercomputing and Networking Center. C.S-B. and A.S.T. are recipients of a scholarship associated with the POWER project (grant nos. POWR.03.02.00-00-I022/16 and POWR.03.02.00-00-I006/17, respectively). This repository is part of the paper "Water will find its way: transport through narrow tunnels in hydrolases", and the other repositories associated to it are Hal (10.5281/zenodo.7966082), hEpx (10.5281/zenodo.7965661), Lip (10.5281/zenodo.7966092) and E470G (10.5281/zenodo.7965881)
DOI: 10.5281/zenodo.7966058
title: Water will find its way: transport through narrow tunnels in hydrolases (Epx protein)

description: Water will find its way: transport through narrow tunnels in hydrolases (Epx protein)

The input files and results used for the paper “Water will find its way: transport through narrow tunnels in hydrolases” are separated in the different folders depending the stage they belong to.



01_Simulations.tar.gz: All the files used to get the data employing Molecular Dynamics simulations.

02_Caver.tar.gz: Caver config used together with the Divide-and-conquer approach to study protein tunnels in long molecular dynamics simulations method (https://doi.org/10.1016/j.mex.2022.101968), and after re-clustering as described in the methods section of the paper.

03_Aquaduct.tar.gz: Aquaduct results for all the MD trajectories.

04_TransportTools.tar.gz: TransportTools results (https://doi.org/10.1093/bioinformatics/btab872).

05_WaterAnalysis.tar.gz: The results from the exact matching analysis were parsed to perform H-bond analysis. Here are the PDBs where the minimum sphere event is present. Also the txt files with the results from the H-bond and contact analyses are here.


Files



01_build_database.py Python3 script to parse the results from the exact matching analysis from TransportTools into a dictionary of transport events. For more detailed information read the script documentation.

Epx.dat Parsed database of transport events for Epx system. Command used: python3 01_build_database.py -c 04_TransportTools/Epx_tt.ini -o Epx.dat
description: This work was supported by the National Science Centre, Poland (grant no. 2017/26/E/NZ1/00548). The computations were performed at the Poznan Supercomputing and Networking Center. C.S-B. and A.S.T. are recipients of a scholarship associated with the POWER project (grant nos. POWR.03.02.00-00-I022/16 and POWR.03.02.00-00-I006/17, respectively). This repository is part of the paper "Water will find its way: transport through narrow tunnels in hydrolases", and the other repositories associated to it are Hal (10.5281/zenodo.7966082), hEpx (10.5281/zenodo.7965661), Lip (10.5281/zenodo.7966092) and E470G (10.5281/zenodo.7965881)
DOI: 10.5281/zenodo.10500692
title: Water will find its way: transport through narrow tunnels in hydrolases (Hal protein)

description: Water will find its way: transport through narrow tunnels in hydrolases (Hal protein)

The input files and results used for the paper “Water will find its way: transport through narrow tunnels in hydrolases” are separated in the different folders depending the stage they belong to.



01_Simulations.tar.gz: All the files used to get the data employing Molecular Dynamics simulations.

02_Caver.tar.gz: Caver config used together with the Divide-and-conquer approach to study protein tunnels in long molecular dynamics simulations method (https://doi.org/10.1016/j.mex.2022.101968), and after re-clustering as described in the methods section of the paper.

03_Aquaduct.tar.gz: Aquaduct results for all the MD trajectories.

04_TransportTools.tar.gz: TransportTools results (https://doi.org/10.1093/bioinformatics/btab872).

05_WaterAnalysis.tar.gz: The results from the exact matching analysis were parsed to perform H-bond analysis. Here are the PDBs where the minimum sphere event is present. Also the txt files with the results from the H-bond and contact analyses are here.


Files



01_build_database.py Python3 script to parse the results from the exact matching analysis from TransportTools into a dictionary of transport events. For more detailed information read the script documentation.

Hal.dat Parsed database of transport events for Hal system. Command used: python3 01_build_database.py -c 04_TransportTools/Hal_tt.ini -o Hal.dat
description: This work was supported by the National Science Centre, Poland (grant no. 2017/26/E/NZ1/00548). The computations were performed at the Poznan Supercomputing and Networking Center. C.S-B. and A.S.T. are recipients of a scholarship associated with the POWER project (grant nos. POWR.03.02.00-00-I022/16 and POWR.03.02.00-00-I006/17, respectively). This repository is part of the paper "Water will find its way: transport through narrow tunnels in hydrolases", and the other repositories associated to it are Epx (10.5281/zenodo.7966059), hEpx (10.5281/zenodo.7965661), Lip (10.5281/zenodo.7966092) and E470G (10.5281/zenodo.7965881)
DOI: 10.5281/zenodo.7966081
title: Water will find its way: transport through narrow tunnels in hydrolases (Hal protein)

description: Water will find its way: transport through narrow tunnels in hydrolases (Hal protein)

The input files and results used for the paper “Water will find its way: transport through narrow tunnels in hydrolases” are separated in the different folders depending the stage they belong to.



01_Simulations.tar.gz: All the files used to get the data employing Molecular Dynamics simulations.

02_Caver.tar.gz: Caver config used together with the Divide-and-conquer approach to study protein tunnels in long molecular dynamics simulations method (https://doi.org/10.1016/j.mex.2022.101968), and after re-clustering as described in the methods section of the paper.

03_Aquaduct.tar.gz: Aquaduct results for all the MD trajectories.

04_TransportTools.tar.gz: TransportTools results (https://doi.org/10.1093/bioinformatics/btab872).

05_WaterAnalysis.tar.gz: The results from the exact matching analysis were parsed to perform H-bond analysis. Here are the PDBs where the minimum sphere event is present. Also the txt files with the results from the H-bond and contact analyses are here.


Files



01_build_database.py Python3 script to parse the results from the exact matching analysis from TransportTools into a dictionary of transport events. For more detailed information read the script documentation.

Hal.dat Parsed database of transport events for Hal system. Command used: python3 01_build_database.py -c 04_TransportTools/Hal_tt.ini -o Hal.dat
description: This work was supported by the National Science Centre, Poland (grant no. 2017/26/E/NZ1/00548). The computations were performed at the Poznan Supercomputing and Networking Center. C.S-B. and A.S.T. are recipients of a scholarship associated with the POWER project (grant nos. POWR.03.02.00-00-I022/16 and POWR.03.02.00-00-I006/17, respectively). This repository is part of the paper "Water will find its way: transport through narrow tunnels in hydrolases", and the other repositories associated to it are Epx (10.5281/zenodo.7966059), hEpx (10.5281/zenodo.7965661), Lip (10.5281/zenodo.7966092) and E470G (10.5281/zenodo.7965881)
DOI: 10.5281/zenodo.7662951
title: Methontology da OntoTurnover (V1)

description: Material usado como base para a construção da ontologia de domínio sobre o turnover.
DOI: 10.5281/zenodo.7662952
title: Methontology da OntoTurnover (V1)

description: Material usado como base para a construção da ontologia de domínio sobre o turnover.
DOI: 10.5281/zenodo.10500955
title: A concrete syntax transformation approach for software language processing

description: This is the dataset for our paper "A concrete syntax transformation approach for software language processing".
DOI: 10.5281/zenodo.10500956
title: A concrete syntax transformation approach for software language processing

description: This is the dataset for our paper "A concrete syntax transformation approach for software language processing".
DOI: 10.25345/c5c24qz68
title: MassIVE MSV000093860 - Spinophilin Islet Immunoprecipitation
title: Second set of data - IP-MS results for spinophilin in islet cells. Spinophilin is an F-actin binding and protein phosphatase 1 (PP1) targeting protein that acts as a scaffold of PP1 to its substrates. Spinophilin knockout (Spino-/-) mice have decreased fat mass, increased lean mass, and improved glucose tolerance, with no difference in feeding behaviors. While spinophilin is enriched in neurons, its roles in non-neuronal tissues, such as beta cells of the pancreatic islets, are unclear. We have corroborated and expanded upon previous studies to determine that Spino-/- mice have decreased weight gain and improved glucose tolerance in two different models of obesity. Using proteomics and immunoblotting-based approaches we identified multiple putative spinophilin interacting proteins isolated from intact pancreas and observed increased interactions of spinophilin with exocrine, ribosomal, and cytoskeletal protein classes that normally act to mediate peptide hormone production, processing, and/or release in Leprdb/db and/or high fat-fed (HFF) models of obesity. Additionally, we have found that spinophilin interacts with proteins from similar classes in isolated islets, suggesting a role for spinophilin in the pancreatic islet. Consistent with a pancreatic beta cell type-specific role for spinophilin, using our recently described conditional spinophilin knockout mice, we found that loss of spinophilin specifically in pancreatic beta cells improved glucose tolerance without impacting body weight in chow-fed mice. Our data further support a role for spinophilin in mediating pathophysiological changes in body weight and whole-body metabolism associated with obesity and provide the first evidence that pancreatic spinophilin protein binding is impacted by obesity and that loss of spinophilin in pancreatic beta cells impacts glucose and insulin actions.
DOI: 10.5281/zenodo.10500978
title: Water will find its way: transport through narrow tunnels in hydrolases (Lip protein)

description: Water will find its way: transport through narrow tunnels in hydrolases (Lip protein)

The input files and results used for the paper “Water will find its way: transport through narrow tunnels in hydrolases” are separated in the different folders depending the stage they belong to.



01_Simulations.tar.gz: All the files used to get the data employing Molecular Dynamics simulations.

02_Caver.tar.gz: Caver config used together with the Divide-and-conquer approach to study protein tunnels in long molecular dynamics simulations method (https://doi.org/10.1016/j.mex.2022.101968), and after re-clustering as described in the methods section of the paper.

03_Aquaduct.tar.gz: Aquaduct results for all the MD trajectories.

04_TransportTools.tar.gz: TransportTools results (https://doi.org/10.1093/bioinformatics/btab872).

05_WaterAnalysis.tar.gz: The results from the exact matching analysis were parsed to perform H-bond analysis. Here are the PDBs where the minimum sphere event is present. Also the txt files with the results from the H-bond analysis are here.


Files



01_build_database.py Python3 script to parse the results from the exact matching analysis from TransportTools into a dictionary of transport events. For more detailed information read the script documentation.

Lip.dat Parsed database of transport events for Lip system. Command used: python3 01_build_database.py -c 04_TransportTools/Lip_tt.ini -o Lip.dat
description: This work was supported by the National Science Centre, Poland (grant no. 2017/26/E/NZ1/00548). The computations were performed at the Poznan Supercomputing and Networking Center. C.S-B. and A.S.T. are recipients of a scholarship associated with the POWER project (grant nos. POWR.03.02.00-00-I022/16 and POWR.03.02.00-00-I006/17, respectively). This repository is part of the paper "Water will find its way: transport through narrow tunnels in hydrolases", and the other repositories associated to it are Hal (10.5281/zenodo.7966082), Epx (10.5281/zenodo.7966059), hEpx (10.5281/zenodo.7965661) and E470G (10.5281/zenodo.7965881)
DOI: 10.5281/zenodo.7966091
title: Water will find its way: transport through narrow tunnels in hydrolases (Lip protein)

description: Water will find its way: transport through narrow tunnels in hydrolases (Lip protein)

The input files and results used for the paper “Water will find its way: transport through narrow tunnels in hydrolases” are separated in the different folders depending the stage they belong to.



01_Simulations.tar.gz: All the files used to get the data employing Molecular Dynamics simulations.

02_Caver.tar.gz: Caver config used together with the Divide-and-conquer approach to study protein tunnels in long molecular dynamics simulations method (https://doi.org/10.1016/j.mex.2022.101968), and after re-clustering as described in the methods section of the paper.

03_Aquaduct.tar.gz: Aquaduct results for all the MD trajectories.

04_TransportTools.tar.gz: TransportTools results (https://doi.org/10.1093/bioinformatics/btab872).

05_WaterAnalysis.tar.gz: The results from the exact matching analysis were parsed to perform H-bond analysis. Here are the PDBs where the minimum sphere event is present. Also the txt files with the results from the H-bond analysis are here.


Files



01_build_database.py Python3 script to parse the results from the exact matching analysis from TransportTools into a dictionary of transport events. For more detailed information read the script documentation.

Lip.dat Parsed database of transport events for Lip system. Command used: python3 01_build_database.py -c 04_TransportTools/Lip_tt.ini -o Lip.dat
description: This work was supported by the National Science Centre, Poland (grant no. 2017/26/E/NZ1/00548). The computations were performed at the Poznan Supercomputing and Networking Center. C.S-B. and A.S.T. are recipients of a scholarship associated with the POWER project (grant nos. POWR.03.02.00-00-I022/16 and POWR.03.02.00-00-I006/17, respectively). This repository is part of the paper "Water will find its way: transport through narrow tunnels in hydrolases", and the other repositories associated to it are Hal (10.5281/zenodo.7966082), Epx (10.5281/zenodo.7966059), hEpx (10.5281/zenodo.7965661) and E470G (10.5281/zenodo.7965881)
DOI: 10.5281/zenodo.10500987
title: Water will find its way: transport through narrow tunnels in hydrolases (hEpx protein)

description: Water will find its way: transport through narrow tunnels in hydrolases (hEpx protein)

The input files and results used for the paper "Water will find its way: transport through narrow tunnels in hydrolases" are separated in the different files depending the stage they belong to.



01_Simulations.tar.gz: All the files used to get the data employing Molecular Dynamics simulations.

02_Caver.tar.gz: Caver config used together with the "Divide-and-conquer approach to study protein tunnels in long molecular dynamics simulations" method (https://doi.org/10.1016/j.mex.2022.101968), and after re-clustering as described in the methods section of the paper.

03_Aquaduct.tar.gz: Aquaduct results for all the MD trajectories.

04_TransportTools.tar.gz: TransportTools results for hEpx and E470G systems together, since we employed the comparative approach to analyze the results with TransportTools (https://doi.org/10.1093/bioinformatics/btab872).

05_WaterAnalysis.tar.gz: The results from the exact matching analysis were parsed to perform H-bond analysis. Here are the PDBs where the *minimum sphere event* is present. Also the txt files with the results from the H-bond analysis are here.


Files



01_build_database.py Python3 script to parse the results from the exact matching analysis from TransportTools into a dictionary of transport events. For more detailed information read the script documentation.

hEpx_E470G.dat Parsed database of transport events for hEpx_E470G system. Command used: python3 01_build_database.py -c 04_TransportTools/hEpx_E470G_tt.ini -o hEpx_E470G.dat


 
description: This work was supported by the National Science Centre, Poland (grant no. 2017/26/E/NZ1/00548). The computations were performed at the Poznan Supercomputing and Networking Center. C.S-B. and A.S.T. are recipients of a scholarship associated with the POWER project (grant nos. POWR.03.02.00-00-I022/16 and POWR.03.02.00-00-I006/17, respectively). This repository is part of the paper "Water will find its way: transport through narrow tunnels in hydrolases", and the other repositories associated to it are Hal (10.5281/zenodo.7966082), Epx (10.5281/zenodo.7966059), Lip (10.5281/zenodo.7966092) and E470G (10.5281/zenodo.7965881)
DOI: 10.5281/zenodo.7965660
title: Water will find its way: transport through narrow tunnels in hydrolases (hEpx protein)

description: Water will find its way: transport through narrow tunnels in hydrolases (hEpx protein)

The input files and results used for the paper "Water will find its way: transport through narrow tunnels in hydrolases" are separated in the different files depending the stage they belong to.



01_Simulations.tar.gz: All the files used to get the data employing Molecular Dynamics simulations.

02_Caver.tar.gz: Caver config used together with the "Divide-and-conquer approach to study protein tunnels in long molecular dynamics simulations" method (https://doi.org/10.1016/j.mex.2022.101968), and after re-clustering as described in the methods section of the paper.

03_Aquaduct.tar.gz: Aquaduct results for all the MD trajectories.

04_TransportTools.tar.gz: TransportTools results for hEpx and E470G systems together, since we employed the comparative approach to analyze the results with TransportTools (https://doi.org/10.1093/bioinformatics/btab872).

05_WaterAnalysis.tar.gz: The results from the exact matching analysis were parsed to perform H-bond analysis. Here are the PDBs where the *minimum sphere event* is present. Also the txt files with the results from the H-bond analysis are here.


Files



01_build_database.py Python3 script to parse the results from the exact matching analysis from TransportTools into a dictionary of transport events. For more detailed information read the script documentation.

hEpx_E470G.dat Parsed database of transport events for hEpx_E470G system. Command used: python3 01_build_database.py -c 04_TransportTools/hEpx_E470G_tt.ini -o hEpx_E470G.dat


 
description: This work was supported by the National Science Centre, Poland (grant no. 2017/26/E/NZ1/00548). The computations were performed at the Poznan Supercomputing and Networking Center. C.S-B. and A.S.T. are recipients of a scholarship associated with the POWER project (grant nos. POWR.03.02.00-00-I022/16 and POWR.03.02.00-00-I006/17, respectively). This repository is part of the paper "Water will find its way: transport through narrow tunnels in hydrolases", and the other repositories associated to it are Hal (10.5281/zenodo.7966082), Epx (10.5281/zenodo.7966059), Lip (10.5281/zenodo.7966092) and E470G (10.5281/zenodo.7965881)
DOI: 10.5281/zenodo.7966059
title: Water will find a way: transport through narrow tunnels in hydrolases (Epx protein)

description: <strong>Water will find a way: transport through narrow tunnels in hydrolases (Epx protein)</strong> <br> The input files and results used for the paper “<em>Water will find a way: transport through narrow tunnels in hydrolases</em>” are separated in the different folders depending the stage they belong to. <strong>01_Simulations.tar.gz:</strong> All the files used to get the data employing Molecular Dynamics simulations. <strong>02_Caver.tar.gz:</strong> Caver config used together with the Divide-and-conquer approach to study protein tunnels in long molecular dynamics simulations method (https://doi.org/10.1016/j.mex.2022.101968), and after re-clustering as described in the methods section of the paper. <strong>03_Aquaduct.tar.gz:</strong> Aquaduct results for all the MD trajectories. <strong>04_TransportTools.tar.gz:</strong> TransportTools results (https://doi.org/10.1093/bioinformatics/btab872). <strong>05_WaterAnalysis.tar.gz:</strong> The results from the exact matching analysis were parsed to perform H-bond analysis. Here are the PDBs where the minimum sphere event is present. Also the txt files with the results from the H-bond analysis are here. <strong>Files</strong> <strong>01_build_database.py</strong> Python3 script to parse the results from the exact matching analysis from TransportTools into a dictionary of transport events. For more detailed information read the script documentation. <strong>Epx.dat</strong> Parsed database of transport events for Epx system. Command used: <em>python3 01_build_database.py -c 04_TransportTools/Epx_tt.ini -o Epx.dat</em>
description: This work was supported by the National Science Centre, Poland (grant no. 2017/26/E/NZ1/00548). The computations were performed at the Poznan Supercomputing and Networking Center. C.S-B. and A.S.T. are recipients of a scholarship associated with the POWER project (grant nos. POWR.03.02.00-00-I022/16 and POWR.03.02.00-00-I006/17, respectively). This repository is part of the paper "Water will find a way: transport through narrow tunnels in hydrolases", and the other repositories associated to it are Hal (10.5281/zenodo.7966082), hEpx (10.5281/zenodo.7965661), Lip (10.5281/zenodo.7966092) and E470G (10.5281/zenodo.7965881)