methods are becoming more promising in this aspect. These
computational methods are usually composed of two subsequent
stages, namely, identifying the binding site and, subsequently, char-
acterizing its druggability [10, 11]. The site identification phase
aims at analyzing the distribution of all hot spots on the target, and
employs both structure-based methods and sequence-based meth-
ods. On the other hand, the druggability of a binding site can be
characterized different druggability indexes, as described below.
In general, binding sites can be classified into three major types.
The first includes catalytic sites or enzymatic binding sites
[12]. These binding sites usually possess specific catalytic functions,
allowing it to interact with a substrate and execute chemical reac-
tions, transforming the substrate into a new product. The second
class comprises allosteric binding sites [13–18], which are not
inducing any catalytic activity, however, interacting with these
sites can indirectly impact the function, dynamics, or distribution
of conformations of the target, which can indirectly modulate its
activity [19]. The third and the most complicated class of binding
sites are usually termed as cryptic binding sites. They are almost
hidden and rarely can appear on the surface of the protein. They
usually occupy a small portion of the conformational ensemble of
the target and are only partly detectable in the unbound target
[20]. Identifying cryptic sites may require a great deal of structural
and conformational analysis of the target (Fig.1).
Binding site recognition methods can hardly identify all poten-
tial binding sites, especially, if the search process involves only a
single static structure. An experimental crystal structure is an aver-
age in time and space of protein dynamics. A binding site can be
easily hidden in a crystal structure, and can be only identified when
its dynamical properties are taken into account. In this context, the
flexibility of the target plays a significant role in binding site forma-
tion and identification [21] and studying these conformational
dynamics is an essential step in this process. One way to study and
reveal these dynamics is to use molecular dynamics (MD)Fig. 1Different types of binding sites include (a) the active site, (b) allosteric site, which can change their
conformation before (pink) and after (blue) binding with allosteric modular, and (c) cryptic binding site, which
can occasionally open (blue)
88 Tianhua Feng and Khaled Barakat