Entangled motifs in membrane protein structures

Salicari, Leonardo and Trovato, Antonio (2023) Entangled motifs in membrane protein structures. [Data Collection]

Collection description

Scripts, input data and results for the "Entangled motifs in membrane protein structures" publication

DOI:	10.25430/researchdata.cab.unipd.it.00000897
Keywords:	membrane proteins; protein domain structures; linking number; entanglement; Gaussian entanglement; bioinformatics
Subjects:	Life Sciences > Genetics, 'Omics', Bioinformatics and Systems Biology: Molecular genetics, quantitative genetics, genetic epidemiology, epigenetics, genomics, metagenomics, glycomics, bioinformatics, computational biology, biostatistics, systems biology proteomics, metab > Bioinformatics Physical:Sciences and Engineering > Condensed Matter Physics: Structure, electronic properties, fluids, nanosciences, biological physics > Statistical physics: phase transitions, noise and fluctuations, models of complex systems, etc. Physical:Sciences and Engineering > Condensed Matter Physics: Structure, electronic properties, fluids, nanosciences, biological physics > Physics of biological systems
Department:	Departments > Dipartimento di Fisica e Astronomia "Galileo Galilei" (DFA)
Depositing User:	Leonardo Salicari
Date Deposited:	22 May 2023 09:23
Last Modified:	22 May 2023 09:23
Creators/Authors:	Creators Email ORCID Salicari, Leonardo leonardo.salicari@phd.unipd.it orcid.org/0000-0003-4444-3885 Trovato, Antonio antonio.trovato@unipd.it orcid.org/0000-0002-1596-9477
Type of data:	Mixed
Collection period:	From To 1 January 2023 1 April 2023
Resource language:	English
Metadata language:	English
Publisher:	Research Data Unipd
Date:	22 May 2023
Copyright holders:	The Author
URI:	https://researchdata.cab.unipd.it/id/eprint/897
Additional details Additional details Creators/Authors: Creators Email ORCID Salicari, Leonardo leonardo.salicari@phd.unipd.it orcid.org/0000-0003-4444-3885 Trovato, Antonio antonio.trovato@unipd.it orcid.org/0000-0002-1596-9477 Type of data: Mixed Collection period: From To 1 January 2023 1 April 2023 Resource language: English Metadata language: English Publisher: Research Data Unipd Date: 22 May 2023 Copyright holders: The Author Last Modified: 22 May 2023 09:23

Available Files

Full Archive

0_pipeline.zip 0_pipeline.zip 0_pipeline.zip Visible to: Anyone Content type: Full Archive Description: Membrane protein dataset scripts and raw tables Metadata Revision: 2 Mime-Type: application/zip License: Creative Commons: Attribution 4.0 File size: 31MB

1_contact_maps.zip 1_contact_maps.zip 1_contact_maps.zip Visible to: Anyone Content type: Full Archive Description: Scripts to compute contact maps for each chain Metadata Revision: 2 Mime-Type: application/zip License: Creative Commons: Attribution 4.0 File size: 3kB

2_structure_modeling.zip 2_structure_modeling.zip 2_structure_modeling.zip Visible to: Anyone Content type: Full Archive Description: Script for modeling structures Metadata Revision: 2 Mime-Type: application/zip License: Creative Commons: Attribution 4.0 File size: 466kB

3_gaussian_enta ... computation.zip 3_gaussian_enta ... computation.zip 3_gaussian_enta ... computation.zip Visible to: Anyone Content type: Full Archive Description: Scripts used for the computation of the Gaussian Entanglement Metadata Revision: 2 Mime-Type: application/zip License: Creative Commons: Attribution 4.0 File size: 28kB

4_ge_results.zip 4_ge_results.zip 4_ge_results.zip Visible to: Anyone Content type: Full Archive Description: Scripts and results tables for the G' computation Metadata Revision: 2 Mime-Type: application/zip License: Creative Commons: Attribution 4.0 File size: 328kB

Data

CM.zip CM.zip CM.zip Visible to: Anyone Content type: Data Description: Contact Map computed Metadata Revision: 2 Mime-Type: application/zip License: Creative Commons: Attribution 4.0 File size: 5MB

ALIGNMENTS.zip ALIGNMENTS.zip ALIGNMENTS.zip Visible to: Anyone Content type: Data Description: Alignments used for the modeling procedure Metadata Revision: 2 Mime-Type: application/zip License: Creative Commons: Attribution 4.0 File size: 1MB

CHAINS_FIX.zip CHAINS_FIX.zip CHAINS_FIX.zip Visible to: Anyone Content type: Data Description: PDB files used for the G' computation Metadata Revision: 2 Mime-Type: application/zip License: Creative Commons: Attribution 4.0 File size: 59MB

Read me

readme.md readme.md readme.md Visible to: Anyone Content type: Readme Description: Readme of the Data repository Metadata Revision: 2 Mime-Type: text/plain License: Creative Commons: Attribution 4.0 File size: 3kB