## 2 Results and Discussion
### Applications
#### Matching two protein structures
Both proteins bind the co-substrate ADP ribose and transfer an acetyl-group from a peptide-substrate to an ADP ribose to form 2'-O-acetyl-ADP-ribose (OAR). The structure of the complex of Hst2 with OAR is known, whereas the structure of the OAR complex with Sir2 is not known. Here we try to locate the OAR-binding pocket on Sir2 in the following way: We first define the OAR-binding epitope as the 20 amino-acid residues identified by [PERSON] _et al._[14] in the structure of Hst2. Then, by using this epitope as query, we search for a match on the structure of Sir2. In this application we test the effectivity of a number of specific and unspecific search modes, each with five different sets of atoms per amino-acid. The results are shown in Figure 6). Run times per search were in the range of 2.3 min to 5.2 min, memory usage between 8 MB and 50 MB. The amino-acid specific search identifies 11 of the 20 residues of the Hst2-epitope also in Sir2 if  
Figure 6: Results of amino-acid specific (left) and unspecific (right) searches for a match of the OAR binding epitope of yeast Hst2 on human Sir2 with various sets of atoms per residue. atoms are included (left part of Figure 6) at a RMSD of 1 A. The unspecific search finds at an RMSD of less than 2 A even 17 residue matches (right part of Figure 6). The 6 residues not found in the specific search are replaced in Sir2 by residues that are not too different (T37(Hst2) \(\rightarrow\) A28(Sir2), F67\(\rightarrow\)A51, T224\(\rightarrow\)S192, L249\(\rightarrow\)A218, Y269\(\rightarrow\)K234, S270\(\rightarrow\)A235). Both search modes show a distinct gap at 11 and 17 matched residues, respectively, giving a natural cutoff for the number of true matches. The non-specific search finds a noise of many false positive matches, while the true positive matches are separated from this noise by distinctly lower RMSD values. Figure 7 shows the parts of Sir2 that have been matched with the OAR binding epitope of Hst2. The residues matched in the unspecific mode (cyan and magenta) delineate the whole binding pocket of OAR, whereas the residues matched in the amino-acid specific mode (magenta) concentrate around the actual enzymatic site where the acetyl-group is transferred from a peptide to the OAR precursor. If the transformation that optimally superimposes the Hst2 epitope with the putative epitope in Sir2 (Step 4 of algorithm) is also applied to the OAR of Hst2, the transformed OAR fits well into the putative epitope pocket of Sir2. It is particularly remarkable that the position of the acetyl-group of OAR is very close to the position of an acetylated Lys residue of a substrate-peptide complexed with Sir2, supporting the correctness of the match. Figure 7: The part of the human Sir2 protein structure (PDB-code 1 MA3) matched with the OAR binding pocket of yeast Hst2. All 17 residues shown as molecular surface have been found as “unspecific” match. A subset of these (magenta) has been matched with the amino-acid specific mode. The molecule in sticks-representation in the center is OAR transformed into the empty binding pocket of Sir2 from the structure of the original complex with Hst2 using the co-ordinate transformation derived from the match (there are two very close OAR positions, derived from the specific and unspecific match, respectively). The grey sticks in the right half are an acetylated Lys residue of a substrate-peptide complexed with Sir2. Identification of a ligand binding site in a database  
This is an example of a typical medium-to-large scale application of EpitopeMatch. We have taken a set of structures of pairs of apo-enzymes and the corresponding holo-enzymes compiled by [PERSON] [16], excluding structures of more than 1000 amino-acids for reasons of memory restriction (see section 2.5.). The resulting set contains 86 pairs of proteins. The pair of holo- (PDB-code 1 AKE) and apo-adenylate-kinase (PDB-code 4 AKE) of _E. Coli_ is part of the set.