Folding of an Entangled Protein

Salicari, Leonardo and Baiesi, Marco and Orlandini, Enzo and Trovato, Antonio (2023) Folding of an Entangled Protein. [Data Collection]

Available Versions of this Item

• Folding of an Entangled Protein. (deposited 10 Mar 2023 07:43)
  • Folding of an Entangled Protein. (deposited 31 Jul 2023 06:42)
    • Folding of an Entangled Protein. (deposited 12 Sep 2023 08:45) [Currently Displayed]

Collection description

Molecular Dynamics trajectories and script files used for the manuscript: "Folding of an Entangled Protein".

DOI:	10.25430/researchdata.cab.unipd.it.00000837
Keywords:	protein folding; linking number; entanglement; Gaussian entanglement; intermediate states; kinetic bottlenecks; misfolding; numerical simulation; molecular dynamics
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 > Computational biology 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:	12 Sep 2023 08:45
Last Modified:	12 Sep 2023 08:45
Creators/Authors:	Creators Email ORCID Salicari, Leonardo leonardo.salicari@phd.unipd.it orcid.org/0000-0003-4444-3885 Baiesi, Marco marco.baiesi@unipd.it orcid.org/0000-0002-4513-9191 Orlandini, Enzo enzo.orlandini@unipd.it orcid.org/0000-0003-3680-9488 Trovato, Antonio antonio.trovato@unipd.it orcid.org/0000-0002-1596-9477
Type of data:	Mixed
Collection period:	From To 29 October 2022 1 March 2023
Resource language:	English
Metadata language:	English
Publisher:	Research Data Unipd
Date:	22 February 2023
Copyright holders:	The Author
URI:	https://researchdata.cab.unipd.it/id/eprint/984
Additional details Additional details Creators/Authors: Creators Email ORCID Salicari, Leonardo leonardo.salicari@phd.unipd.it orcid.org/0000-0003-4444-3885 Baiesi, Marco marco.baiesi@unipd.it orcid.org/0000-0002-4513-9191 Orlandini, Enzo enzo.orlandini@unipd.it orcid.org/0000-0003-3680-9488 Trovato, Antonio antonio.trovato@unipd.it orcid.org/0000-0002-1596-9477 Type of data: Mixed Collection period: From To 29 October 2022 1 March 2023 Resource language: English Metadata language: English Publisher: Research Data Unipd Date: 22 February 2023 Copyright holders: The Author Last Modified: 12 Sep 2023 08:45

Available Files

Full Archive

entangled_folding.zip entangled_folding.zip entangled_folding.zip Visible to: Anyone Content type: Full Archive Description: Cython/Python scripts used to analyse Molecular Dynamics trajectories Metadata Revision: 6 Mime-Type: application/zip License: Creative Commons: Attribution 4.0 File size: 1MB

Data

example_input_files.zip example_input_files.zip example_input_files.zip Visible to: Anyone Content type: Data Description: Example of input files for the Molecular Dynamics simulations perfomed with LAMMPS software Metadata Revision: 11 Mime-Type: application/zip License: Creative Commons: Attribution 4.0 File size: 14kB

equilibrium_trajectories.zip equilibrium_trajectories.zip equilibrium_trajectories.zip Visible to: Anyone Content type: Data Description: Molecular Dynamics trajectories for the equilibrium case Metadata Revision: 11 Mime-Type: application/zip License: Creative Commons: Attribution 4.0 File size: 1GB

kinetics_1_trajectories.zip kinetics_1_trajectories.zip kinetics_1_trajectories.zip Visible to: Anyone Content type: Data Description: Molecular Dynamics trajectories for the kinetic case (part 1) Metadata Revision: 13 Mime-Type: application/zip License: Creative Commons: Attribution 4.0 File size: 3GB

kinetics_2_trajectories.zip kinetics_2_trajectories.zip kinetics_2_trajectories.zip Visible to: Anyone Content type: Data Description: Molecular Dynamics trajectories for the kinetic case (part 1) Metadata Revision: 13 Mime-Type: application/zip License: Creative Commons: Attribution 4.0 File size: 2GB

Q_G_timeseries.zip Q_G_timeseries.zip Q_G_timeseries.zip Visible to: Anyone Content type: Data Description: Fraction of native contacts (Q) and average Gaussian entanglement <G'> timeseries for all trajectories Metadata Revision: 6 Mime-Type: application/zip License: Creative Commons: Attribution 4.0 File size: 16MB

exponential_fit.zip exponential_fit.zip exponential_fit.zip Visible to: Anyone Content type: Data Description: CSV with exponential fit parameters of contact formation probabilities Metadata Revision: 9 Mime-Type: application/zip License: Creative Commons: Attribution 4.0 File size: 21kB

Read me

readme_general.pdf readme_general.pdf readme_general.pdf Visible to: Anyone Content type: Readme Description: General Readme Metadata Revision: 10 Mime-Type: application/pdf License: Creative Commons: Attribution 4.0 File size: 37kB

datasets_list_description.txt datasets_list_description.txt datasets_list_description.txt Visible to: Anyone Content type: Readme Description: List with brief descriptions of the directories containing Molecular Dynamics trajectories Metadata Revision: 9 Mime-Type: text/plain License: Creative Commons: Attribution 4.0 File size: 715B