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

This object 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.

• 2022-01-01 to 2024-04-01

• 2024

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

OpenMM 8.1
AmberTools 19.12
Cpptraj 4.14.0
PDB2PQR 3.6.1
CHARMM-GUI
Amber 21

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

• data

• English

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

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

Creative Commons Attribution 4.0 International Public License

• UC Regents

Under copyright (US)

Use: This work is available from the UC San Diego Library. This digital copy of the work is intended to support research, teaching, and private study.

Constraint(s) on Use: This work is protected by the U.S. Copyright Law (Title 17, U.S.C.). Use of this work beyond that allowed by "fair use" or any license applied to this work requires written permission of the copyright holder(s). Responsibility for obtaining permissions and any use and distribution of this work rests exclusively with the user and not the UC San Diego Library. Inquiries can be made to the UC San Diego Library program having custody of the work.

Research Data Curation Program, UC San Diego, La Jolla, 92093-0175 (https://lib.ucsd.edu/rdcp)

2024-06-25