DOI: 10.5281/zenodo.13137463
title: Ace-Ala-Xaa-Ala-NH2 sasa and Phi,Psi surfaces

description: ******************************************************************************                               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******************************************************************************