The present manuscript describes a novel 3D-QSAR alignment free method (QuBiLS-MIDAS Duplex) based on
algebraic bilinear, quadratic and linear forms on the k
two-tuple spatial-(dis)similarity matrix. Generalization schemes for the
inter-atomic spatial distance using diverse (dis)-similarity measures are discussed. On the other hand, normalization approaches
for the two-tuple spatial-(dis)similarity matrix by using simple- and double-stochastic and mutual probability schemes are
introduced. With the aim of taking into consideration particular inter-atomic interactions in total or local-fragment indices, path
and length cut-off constraints are used. Also, in order to generalize the use of the linear combination of atom-level indices to yield
global (molecular) definit...