SuMo: A Tool for Protein Function Inference Based on 3D Structures Comparisons - Identification of Ligand Binding Site and Protein-Protein Interaction Area - page 4

1.2.2 New De fi nition of SuMo Objects

The set of object was not modified since the first version of the software (Jambon
et al. 2003 ) and since the original release, we have improved this set to increase the
efficacy and the accuracy of the SuMo software. The strategy is to use a minimal
number of different types of object and to have also fewer objects that the previous
set to compare a complete surface versus a large database like the PDB. This calcula-
tion requires large computer resources and may take a long time to compute or
requires the use of a super computer. That is why, we have tried to reduce the number
of object and thus drastically decreasing the combinatorial number of superposition
to score. The new set has 10 different types of objects versus 15 for the first one.
The first set (Jambon et al. 2003 ) described hydrogen bonds with an object called
“delta plus” and this object is placed on the position of the receptor atom of the hydro-
gen bond. This position is computed by extension in the direction of the bond hetero
atom - hydrogen of 1.8 Å. This description induces two problems, the first one is
about the flexibility of the side chain, a small variation of the direction of the hydrogen
can displaced the object to 5 Å and cannot match for calculation. Side chain of amino
acid could generate a large number of hydrogen bonds and all bonds cannot be treated.
We decided to not describe hydrogen bond, by this way, on the new set.
We decide to focus on the chemical function of amino acid and to homogenously
treat all residues. The backbone is described by a new object called “carbon alpha”
centered on the carbon alpha of each amino acid, instead of a “delta plus” extended
from the N-H bond, one “delta minus” centred on the oxygen of the hydroxyl and
just for glycine residue a object called “glycine polar” on the nitrogen of the backbone.
For hydrophobic moiety, we put one object “hydrophobic aliphatic” in the centred
of bond C-C of the side chain (carbon alpha is not included in this calculation).
One exception is made for the alanine residue, one “hydrophobic aliphatic” is centred
on the methyl. We define ten types of objects centered on chemical function like
hydroxyl, carboxylic acid, amine. For hydrophobic or amine function we define the
aliphatic or the aromatic object type, except for hydroxyl because the capacity for
this function to make hydrogen bond is roughly the same for the two types. We also
create the following objects : amide, thiol and carboxylic acid. The guanidinium
moiety could be described with aromatic amine and hydrophobic, but we prefer to
create a specific object for this function due to the particularity of the reactivity of
the residue. The group of residue composed with aromatic cyclic was described
with “hydrophobic aromatic” and “amine aromatic” objects. The hydrophobic object
was positioned at the barycentre of the cycle. In the case of tryptophan residue
one object was positioned was each cycle. Each nitrogen atoms of aromatic cycle
were described by an aromatic amine object and centred on it. For the tyrosine resi-
due the hydroxyl object was added centred on the oxygen atom. Figure 1.1 lists the
nature and the position of object for each residue. The SuMo software has weighting
value of the different object. All objects have the same weight (1) instead of “carbon
alpha” with the value of (0.1). This choice was made in order to avoid to give to the