How to extract the atomic coordinates of a specific amino acid from a pdb file
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Hello, Is it possible in Matlab bioinformatics tool, to extract the coordinates of a specific amino acid like lysine and store it in a Matrix.. There will be many lysine residues in a protein. How to store the atomic coordinates of each and every lysine residue from a protein in matrices Lysine1_coordinates, Lysine 2_coordinates and so on from a pdb file using Matlab?
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Arthur Goldsipe 2023년 2월 16일
What is your definition for the location of lysine amino acid? The reason I ask is that a PDB file contain information about the coordinates of specific atoms, not amino acids. As I'm sure you know from the other questions you've already posted, you can use getpdb to access this information in MATLAB. This information includes whether specific atoms are part of a lysine (from the resName field) and which amino acide in the seuqence (from the resSeq field), as well as the coordinates in the X, Y, and Z fields.
My assessment is that this question is a bit too general right now for you to get much help. I suggest you to attempt to sketch out what you want to do in more detail in a combination of MATLAB code and pseudocode. Then, perhaps we can offer more specific advice on whatever parts you're stuck on.
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