Ace-Ala-Xaa-Ala-NH2 sasa and Phi,Psi surfaces

******************************************************************************                               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: [e-mail]******************************************************************************

******************************************************************************
查尔斯·R·沃茨实验室（Charles R. Watts Lab）
蛋白质动力学数据分布（Protein Dynamics Data Distribution）
******************************************************************************

### 内容说明
本目录包含与下述研究论文相关的数据：
Burns,WA;Lovas,S;Watts,CR. 《基于Ac-Ala-Xaa-Ala-NH2体系与CHARMM36m力场模拟的蛋白源性α-氨基酸的溶剂可及表面积随Φ、Ψ二面角空间探索范围的变化规律》，《国际分子科学杂志》（International Journal of Molecular Sciences, IJMS）2024年，已提交。
该数据来自健康伙伴研究所（Healthpartners Institute）的查尔斯·R·沃茨实验室。数据被整理为多个CSV文件，每个文件均包含蛋白质动力学相关信息。

### 文件格式
每个CSV文件采用如下格式：
Time,SASA-FULL,SASA-BACKBONE,SASA-SIDECHAIN,Phi,Psi,Residue,CLUSTER
各字段定义如下：
- Time：数据记录的时间点
- SASA-FULL：全蛋白溶剂可及表面积（Solvent Accessible Surface Area, SASA）
- SASA-BACKBONE：蛋白主链溶剂可及表面积
- SASA-SIDECHAIN：蛋白侧链溶剂可及表面积
- Phi：二面角Φ
- Psi：二面角Ψ
- Residue：被测残基名称及以零基索引标记的位置
- CLUSTER：该残基对应的二级结构簇

### 数据示例
以下为数据格式示例：
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

### 文件列表
本目录提供的CSV文件列表如下：
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

每个文件对应不同的残基数据。此外目录内还包含一个名为Probability Surface的子目录，其中存储了以1度为间隔分箱后的各角度测量值的平滑概率，采用Lovell 2003年提出的算法进行平滑处理。

### 使用方式
该数据可导入多种软件包进行后续分析，包括但不限于：
- Python（pandas、numpy）
- R（data.table、readr）
- MATLAB
- Microsoft Excel

### 许可协议
本数据采用知识共享署名4.0国际许可协议（Creative Commons Attribution 4.0 International, CC BY 4.0）进行授权。您可自由共享和改编本数据，但需给出适当署名。使用本数据时，请引用如下DOI：10.5281/zenodo.13137464。本数据不提供任何明示或暗示的担保。

### 联系方式
如有任何与数据相关的咨询或问题，请联系：
查尔斯·R·沃茨实验室
神经外科系
健康伙伴/帕克尼科莱特/卫理公会医院
邮箱：[e-mail]