p

p

p

s. Discovering the protein functional sites based on the whole

pattern is mainly based on the sequence homology alignment

es. Through an alignment, it is possible to annotate and discover

ons of a novel protein as well as the functional sites. This process

the protein function annotation [Loewenstein, et al., 2007;

epas, et al., 2017; Mahlich, et al., 2018]. This method has been

sed; for instance, the primary sequence comparison can enhance

in function annotation performance in addition to the use of the

n structuring technology [Whisstock and Lesk, 2003; Shatsky, et

.

cting and discovering protein functional sites based on sub-

s or peptides is an exercise of the local protein function

n. This study includes the discovery of the protease cleavage sites

n, et al., 2003; Yang and Berry, 2004; Berry, et al., 2004;

gse, et al., 2005; Yang, et al., 2005; Yang and Thomson, 2005;

d Yang, 2006, Yang and Hammer, 2007; Maji and Das, 2010;

Das, 2010b; Cabuk, et al., 2018; Betancur-Ancona, et al., 2018]

discovery of the post-translational modification sites [Lu, et al.,

ost, et al., 2016; Ivanisenko, et al., 2019]. This kind of research

cal protein structures, such as the amino acid composition in the

cleaved peptides or the posttranslational modified peptides. Such

collects two sets of peptides. One set is composed of the

ntally verified peptides and the other is composed of the null

A null peptide is such a peptide in which there is no

ntally verified protein functional site.

molecular interaction discovery problem

ecular interaction within a biological system is a complex issue.

raction can happen between a biological system and some

mental factors as well as within a biological system. For instance,

ction relationship between a single nucleotide polymorphism and

nvironment has been examined for the pregnant women in