****************************************************************************** Charles R. Watts Lab Protein Dynamics Data Distribution ****************************************************************************** Contents-------- This directory contains data associated with the research paper titled: Burns,WA;Lovas,S;Watts,CR. "Dynamic Solvent Accessible Surface Areas of Proteogenic α-Amino Acids as a Function of Explored Φ,Ψ Dihedral Angle Space Modeled Using the Ac-Ala-Xaa-Ala-NH2 System and CHARMM36m Force Field" International Journal of Molecular Sciences (IJMS) 2024; Sumbitted from the Charles R. Watts Lab at Healthpartners Institute. The data is organized into multiple CSV files, each containing information about protein dynamics. File Format----------- Each CSV file contains data in the following format: Time,SASA-FULL,SASA-BACKBONE,SASA-SIDECHAIN,Phi,Psi,Residue,CLUSTER The columns are defined as follows: Time : The time point at which the data was recorded. SASA-FULL : Solvent Accessible Surface Area for the full protein. SASA-BACKBONE : Solvent Accessible Surface Area for the protein backbone. SASA-SIDECHAIN : Solvent Accessible Surface Area for the protein side chain. Phi : Dihedral angle Φ. Psi : Dihedral angle Ψ. Residue : The name of the residue being measured and position with zero based indexing. CLUSTER : The secondary structure cluster associated with the residue. Example Data------------ Below is an example of the data format: Time,SASA-FULL,SASA-BACKBONE,SASA-SIDECHAIN,Phi,Psi,Residue,CLUSTER 200002.0,104.19,45.93,58.26,-60.4,152.19,ALA-3,Beta 200004.0,103.76,43.14,60.62,-98.82,159.36,ALA-3,Beta 200006.0,102.23,45.05,57.18,-142.54,-179.97,ALA-3,Beta 200008.0,104.6,48.57,56.03,-158.17,158.18,ALA-3,Beta 200010.0,107.55,47.68,59.87,-164.53,157.51,ALA-3,Beta 200012.0,104.79,33.72,71.07,-88.1,113.28,ALA-3,Beta File List--------- The following is a list of the CSV files provided in this directory: Ala.csv Arg:NH.csv Asp:H.csv Cys-Cys.csv Glu:H.csv His:ND1.csv Leu.csv Met.csv Arg.csv Asn.csv Cys-.csv Gln.csv Gly.csv His:NE2.csv Lys.csv Phe.csv Arg:NE.csv Asp.csv Cys.csv Glu.csv His+.csv Ile.csv Lysn.csv Pro:cis.csv Arg:NH.csv Asp:H.csv Cys-Cys.csv Glu:H.csv His:ND1.csv Leu.csv Met.csv Pro:trans.csv Trp.csv Tyr-.csv Tyr.csv Ser.csv Thr.csv Val.csv Each file contains similar data but for different residues. There is also a directory inside called Probability Surface. This contains all the smoothed probability of each angular measurment binned to 1 degree and smoothed using the algorithm from Lovell 2003. Usage----- The data can be read into a variety of software packages for further analysis, including but not limited to: - Python (pandas, numpy) - R (data.table, readr) - MATLAB - Microsoft Excel License------- This data is liscences under the Creative Commons Attribution 4.0 International (CC BY 4.0) liscence. You are free to share and adapt the data,provided you give appropriate credit. When using this data, please cite as follows below: The data comes with no warranty, express or implied.please cite the following DOI: 10.5281/zenodo.13137464. Contact------- For any inquiries or issues related to the data, please contact: Charles R. Watts Lab Department of Neurosurgery Healthpartners/Park Nicollet/Methodist Hospital Email: charles.watts@parknicollet.com******************************************************************************