Table 4.

CADD applications in RAS-related structure and binding sites identification.

CADD Methods	Results	References
Homology modeling	The 3D structure of RASSF2	[51]
Molecular dynamics simulation	The stability of the prediction model	[53]
Template-based protein–protein complex structure prediction algorithm (PRISM)	The structure of KRAS4B-GTP homodimer	[55]
AlphaFold	Models of 145 RAS superfamily members	[57]
Web server (Sitehound-Web)	Top 10 binding pockets on RASSF2	[51]
Probe-based molecular dynamics (PMD) simulation	Five potential druggable sites (S1–S3, Subsite 1 and Subsite 2) on KRAS	[53]
Fragment-based approach (FTMAP)	Three potential allosteric sites (P1–P3) on RAS	[67]
Multiple solvent crystal structures (MSCS)	Eight potential binding sites (Cluster 1–Cluster 8) on HRAS	[69]