PCA
Issue #690
new
I don't understand PCA of structures. There are three dimensional structures but there are a lot of PCs. As I know, there are at most three PCs for three dimensions. In documentation, you mention 915 eigenvalues. Does it mean there are 915 PCs? If it is so, could you give more details about PCA?
A molecular structure is not three dimension but 3N dimension, where N is the number of atoms. This is just a mathematical concept not necessarily means physical high dimension.
There are a few papers/book that may help you understand:
Jolliffe, I. T. Principal Component Analysis. (2002) Springer Series in Statistics.
Caves, L. S., et al., Locally accessible conformations of proteins: multiple molecular dynamics simulations of crambin. (1998) Protein Sci, 7:649-666.
van Aalten, et al., Protein dynamics derived from clusters of crystal structures. (1997) Biophys J, 73:2891-2896.
Amadei et al., Essential dynamics of proteins. (1993) Proteins, 17:412-425.
Ringnér, M. What is principal component analysis? (2008) Nature Biotechnology, 26:303-304.