Taylor, Bryn C.; Lee, Christopher T.; Amaro, Rommie E. (2019). Data from: Structural basis for ligand modulation of the CCR2 conformational landscape. UC San Diego Library Digital Collections. https://doi.org/10.6075/J0QZ289Q

This object contains the molecular dynamics trajectories and analysis scripts used in the paper “Structural basis for ligand modulation of the CCR2 conformational landscape”. The purpose of this object is to share the simulation data used to build the Markov state models and the methods used to analyze the models and data.

• 2017 to 2018

• 2019

• Lee, Christopher T.
• Taylor, Bryn C.

• Amaro, Rommie E.

The python and python package versions used to generate this data are:
python version 2.7
pyemma version 2.4
mdtraj version 1.9.1
numpy version 1.11.0
matplotlib 2.0.0
pandas version 0.20.1
To create a virtual environment with these libraries, please use the envrionment files in this object.

This work was supported in part by the Director’s New Innovator Award Program NIH DP2OD007237, the National Biomedical Computation Resource (NBCR) NIH P41-GM103426, and the National Science Foundation through XSEDE supercomputing resources provided via TG-CHE060073 to R.E.A. C.T.L. also acknowledges support from the NIH Molecular Biophysics Training Program (T32-GM008326) Anton 2 computer time was provided by the Pittsburgh Supercomputing Center (PSC) through Grant R01GM116961 from the National Institutes of Health. The Anton 2 machine at PSC was generously made available by D.E. Shaw Research.

• Biophysics
• C-C chemokine receptor type 2 (CCR2)
• G protein-coupled receptor
• Markov state model
• Molecular dynamics

• data
• text

• English

Doi: https://doi.org/10.6075/J0QZ289Q

Primary associated publication

• Bryn C. Taylor, Christopher T. Lee, Rommie E. Amaro (2019). Structural basis for ligand modulation of the CCR2 conformational landscape. Proceedings of the National Academy of Sciences Apr 2019, 116 (17) 8131-8136. https://doi.org/10.1073/pnas.1814131116
• Taylor, Bryn C and Lee, Christopher T and Amaro, Rommie E (2018). Structural basis for ligand modulation of the CCR2 conformational landscape. bioRxiv. https://doi.org/10.1101/392068

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)

2023-06-06