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About this collection

Extent

1 digital object.

Cite This Work

Stokely, Andrew M.; Votapka, Lane W.; Hock, Marcus T.; Teitgen, Abigail E.; McCammon, J. Andrew; McCullough, Andrew D.; Amaro, Rommie E. (2024). Data from: NetSci: A Library for High Performance Biomolecular Simulation Network Analysis Computation. UC San Diego Library Digital Collections. https://doi.org/10.6075/J0S46S50

Description

This collection contains trajectory and molecular dynamics simulation output data for NetSci: A Library for High Performance Biomolecular Simulation Network Analysis Computation. Specifically, proteinG and the SERCA pump were simulated to generate trajectories for generalized correlation analysis of biomolecular allosteric motion. In each case, the raw trajectories were stripped of irrelevant atoms, and then analyzed. Both full trajectories and stripped trajectories, as well as topology files and preprocessing scripts, are included here.

Creation Date

• 2022-01-01 to 2024-04-01

Date Issued

• 2024

Authors

• Amaro, Rommie E.
• Hock, Marcus T.
• McCammon, J. Andrew
• McCullough, Andrew D.
• Stokely, Andrew M.
• Teitgen, Abigail E.
• Votapka, Lane W.

Topics

• Allostery
• Correlation motion
• Generalized correlation
• Molecular dynamics
• Mutual information
• Network analysis
• Protein G
• SERCA pump

Formats

View formats within this collection

• data
• text

Language

• English

Identifier

Identifier: Abigail E. Teitgen: https://orcid.org/0000-0002-5134-7261

Identifier: Andrew D. McCullough: https://orcid.org/0000-0002-1708-5675

Identifier: Andrew M. Stokely: https://orcid.org/0000-0002-3750-5323

Identifier: J. Andrew McCammon: https://orcid.org/0000-0003-3065-1456

Identifier: Lane W. Votapka: https://orcid.org/0000-0002-0865-5867

Identifier: Marcus T. Hock: https://orcid.org/0000-0001-6071-5655

Identifier: Rommie E. Amaro: https://orcid.org/0000-0002-9275-9553

Related Resources

Software

• Github repository of Netsci Manuscript Analysis Software: https://github.com/netscianalysis/netsci_paper.git

Other resource

• Github repository of Netsci software: https://github.com/netscianalysis/netsci.git

Collection image

• Image source: Marcus T. Hock, Lane W. Votapka. "The SERCA pump with residues highlighted by correlation to bound ATP nucleotide."