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Data from: Allostery through the Computational Microscope: cAMP Activation of a Canonical Signalling Domain

Component

Molecular dynamics parameters, initial coordinates, and scripts

File Size
  • 2.25 MB
File Format
  • GZIP
Scope And Content

This component contains the files required to perform molecular dynamics simulations from scratch using the Amber molecular dynamics software package. This unit contains the parameter and initial coordinate files need to simulate the four starting systems, fully solvated. The four systems representing both the active and inactive conformations of the cyclic-nucleotide binding domain with and without cAMP bound. Additionally, the data set contains the input files used with Amber to perform system minimization, equilibration, and production run.

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Molecular dynamics trajectories

File Size
  • 12.2 GB
File Format
  • TAR
Scope And Content

This component contains the molecular dynamics trajectories used to construct the Markov state models presented in the paper. The trajectories are presented in the .dcd format, and contain only the atomic coordinates for the protein studied (i.e. no solvent or ligand). The corresponding .pdb file required for visualization using a program like VMD are included.

Each trajectory is labelled as follows: Starting_system-system_state-simulation_run-rep_number.alpro.dcd.

'Starting_system' identifies the family of simulations to which the trajectory belongs, either RAIaB or RAIaH, and 'system_state' identifies whether cAMP was bound to the system during the simulations. 'System_state-simulation_run' identifies the type and architecture used for each molecular dynamics simulation with AS identifying Anton simulations, IS identifying initial sampling simulations using GPU accelerated Amber, and PC identifying adaptive sampling runs using GPU accelerated Amber. 'Rep_number' indicates an independent sampling run with unique initial velocities.

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Model building work and scripts

File Size
  • 6.1 GB
File Format
  • GZIP
Description

This data set is effectively the “lab notebook” of the Markov state models, analysis, and scripts utilized in the associated paper. The objective of this component is not to provide a step-by-step procedure to reproduce the work presented in the paper but to be the equivalent of "showing your work”. Specific questions regarding scripts or intermediate models can be directed to the authors of the associated paper.

Scope And Content

This component contains a snapshot of the scripts used and analyses performed in the paper. It also contains many of intermediate models and alternate analyses not discussed in the paper.

Technical Details

Many of the Python (2.7.x) scripts included in this component are dependent on libraries not included in this data set, but which are publicly available:
SciPy 0.10.1
NetworkX 1.9.1
matplotlib 1.1.1
Additionally, this work was done with MSMBuilder 2.51, which is not included in this package.

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Collection
Cite This Work

Malmstrom, Robert D.; Kornev, Alexandr P.; Taylor, Susan S.; Amaro, Rommie E. (2015). Data from: Allostery through the computational microscope: cAMP activation of a canonical signalling domain. UC San Diego Library Digital Collections. https://doi.org/10.6075/J0Z60KZS

Description

This object contains the molecular dynamics trajectories scripts and models used in the paper “Allostery through the computational microscope: cAMP activation of a canonical signaling domain”. The purpose of this object is to share the simulation data used to build the models and to show how the models presented in the paper were constructed and analyzed.

Creation Date
  • 2014-08-24
Date Issued
  • 2015
Authors
Co Principal Investigators
Note

Funding information: This work was funded in part by the National Institutes of Health (NIH) through the NIH Director’s New Innovator Award Program (DP2-OD007237 to REA, R01-GM034921 to S.S.T.) and an NSF XSEDE supercomputer resources grant (RAC CHE060073N to R.E.A.). Funding from the National Biomedical Computation Resource (NBCR), NIH P41 GM103426 from the National Institutes of Health, is gratefully acknowledged. Anton computer time was provided by the Pittsburgh Supercomputing Center (PSC) and the National Center for Multiscale Modeling of Biological Systems (MM Bios) (grant P41GM103712-S1 from the National Institutes of Health). D.E. Shaw Research generously made the Anton machine at PSC available.

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Format

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Identifier

Doi: https://doi.org/10.6075/J0Z60KZS

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License

Creative Commons Attribution 4.0 International Public License

Rights Holder
  • UC Regents
Copyright

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.

Digital Object Made Available By

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

Last Modified

2023-06-01