Chemistry Reference
In-Depth Information
Table 9.3
Geometric
characteristics of pockets of
bovine recovering identified
using CASTp tool
Area (Å
2
)
Volume (Å
3
)
Pocket ID
23
168.4
306.1
22
174.0
258.4
21
185.1
139.8
20
164.1
142.4
19
61.70
67.40
18
138.0
112.1
Fig. 9.6
Pockets snapshots for bovine recoverin identified using Fpocket. The protein is presented
in
grey
and identified pocket are colored
there is the case. The output of Fpocket returns different files containing informa-
tion about the identified pockets ranked upon their putative capacity to bind a small
molecule. One of this output files is a PDB file containing all atoms used for pocket
detection. Another output file provides statistics about each pocket listing different
characteristics and scores of pockets identified on the surface of the protein. The re-
sults may be visualized using PyMol or VMD software. Fpocket identifies 11 pockets
for bovine recoverin, as presented in Fig.
9.6
.
Pocket characterization includes the computation of numerous descriptors, the
most important from my point of view being the following (Le Guilloux et al.
2009
):
(i) hydrophobicity score measuring the hydrophobic character of the pocket, (ii)
polarity score that, contrary to hydrophobicity score, measures the hydrophilic char-
acter of the pocket, (iii) charge score taking into account the charge for all amino acids
in the pocket, (iv) local hydrophobic density score identifying if the binding pocket
contains local parts that are rather hydrophobic and (v) the volume of the binding
pocket computed using a MonteÂCarlo algorithm that summarize the full volume
occupied by all alpha sphere in the given pocket. A pocket score is assigned for ev-
ery pocket tacking into account the values of all the descriptor used for computation.
Table
9.4
contains the mentioned above descriptors for the 11 pockets identified by
Fpocket for bovine recoverin.
