I encountered some problems in the process of ResPRE building the contact matrix.

[cuilei]

Dear Zhang Yang Lab:
Hello, I encountered some problems in the process of ResPRE building the contact matrix.

1. Download the protein structure file in the PDB. The PDBID of this protein is 1F88. Its sequence length is 348, as shown in Figure 1. But only 338 residues have structural information that can be used to calculate contacts. 10 residues are missing as shown in Figures 2 and 3.
In this case, when constructing the contact matrix, should the dimensions of the contact matrix be 348*348 or 338*338?

Sincerely hope to get your answers. Thank you!

[robpearc]

ResPRE predicts contact maps starting from the amino acid sequence, so it shouldn't be affected by missing regions in the PDB structure. If you input the full amino acid sequence, then the contact matrix will be 348x348. However, if you know the native structure of your protein, you probably don't need to use ResPRE to predict the contact map, as this can be directly taken from the PDB structure, which will be more accurate.