https://github.com/bresmegroup/Buffer-SAP_BSAP

SAP可通过Discovery Studio获得

https://www.doc88.com/p-9092653625430.html?r=1

Prediction of Aggregation Prone Regions of Therapeutic Proteins

Here

(1) SAA of side chain atoms within radius R is computed at each simulation snapshot.

(2) SAA of the side chain of fully exposed residue (say for amino acid “X”) is obtained by calculating the SAA of side chains of the middle residue in the fully extended conformation of tripeptide “Ala-X-Ala”. These SAA values for side chains of fully exposed residues are given in Table 1.

(3) Residue hydrophobicity is obtained by normalizing the hydrophobicity scale of Black and Mould. (49) The scale is normalized such that Glycine has a hydrophobicity of zero (values shown in Table 1). Therefore, amino acids that are more hydrophobic than Glycine are positive and less hydrophobic than Glycine and are negative on the hydrophobic scale.

Table 1. Hydrophobicity, Normalized Hydrophobicity, and SAA of Fully Exposed Side Chains for Different Residuesa