Distance Matrix Calculation Report

Objective

Calculate the minimal Euclidean distance between the two closest atoms of any two positions in a protein coordinate dataset.

Dataset Description

The dataset contains X, Y, and Z coordinates for 856 positions of protein atoms.

Approach

1. Imported the dataset from an Excel file.
2. Created a function to compute Euclidean distance between two points.
3. Extracted unique positions and initialized an empty distance matrix.
4. For each pair of positions, computed the pairwise Euclidean distances between their atoms using the defined function.
5. Recorded the minimal distance between the positions in the distance matrix.
6. Saved the distance matrix as a CSV file.

Results

The code successfully calculated the minimal Euclidean distance between the closest atoms of any two positions in the protein coordinate dataset. The resulting distance matrix captures these distances in a clear and organized format, providing valuable insights into the spatial relationships between protein atoms.

Conclusion

This code aids in understanding the proximity of atoms across different positions in the protein. The distance matrix serves as a valuable resource for analyzing interatomic distances, aiding in tasks such as identifying potential binding sites or investigating structural changes within the protein.