3DMSS-Sites : Frequently Asked Questions
- Q1: I do not
get results although I know either that the query motif is present in
the bank PDB structures or that the two structures are similar ?
- A1: There are several answers to this question:
- As Escan and CSRre preform their search at the atomic level. If the
similarity is too loose, it can exceed the RMSd threshold level. You can
increase this threshold to get looser similarity. If you search for a
very loose similarity at the fold level, you should use YAKUSA, SA-Search (structure
against PDB), DALI or CE (structure against PDB or structure
against structure), which are better suited for this task.
- If searching a query motif against PDB50 or PDB70, the protein you look for is perhaps missing in the PDB50 or PDB70 collections. In that case, you should click on the "equivalent structures" links of matches in the ouput, as for each PDB match, you can see the very similar structures to this PDB file that have been evinced from PDB50 (or PDB70). If you search for a site in a particular structure, you should not choose PDB50 or PDB70, but instead paste its PDB Id in the "raw bank data" text area.
- Q2: With Escan
method in the mode "query against bank PDB50 or PDB70", I get a lot of
matches all from the same protein, differing only by one or two atoms ?
- A2: As Escan does an exhaustive search, it will display all matches with the same number of atoms (matches are sorted by their scores, i.e. simply the number of matching atoms). In fact, in that cases, all solutions should contains a "kernel" with the same atoms, and additional matching atoms are added by escan as they respect the constraint in RMSD. You could reduce the value of the RMS deviation in order to get a "closer" match, or alternatively, set the "Max # matches" parameter to 1, in order to get only one solution per structure of the bank (the best solution).
- Q3: I don't get
matches for my protein when the "Catalytic Site Atlas" is given as the
query ?
- A3: The Catalytic Site Atlas (CSA) bank of site we use in the 3DMSS-Sites server contains only the sites of CSA which are validated and defined at the atom level in existing structures (i.e. not the putative PSIBLAST sites which are also given in the CSA home page, as they are only infered by sequence similarity). It is possible a structure does not contain any. A second possibility is that the input parameters may be un-adapted. See Question1
- Q4: Why does it
takes so long to compare my query motif to the PDB50 or PDB70 database ?
- A3: Using CSRre, the computational time can be long as
one day for a large query against a bank, therefore Escan is the default method used when searching
against a bank structure (PDB50 or PDB70). Nevertheless, Escan can require much longer time than CSRre when comparing a large "motif" (an entiere structure) against another entiere structure.
- Q5: How can I
figure which motif sites/bank structures are used in the 3DMSS-Sites
server ?
- A3: Two answers to this question:
- For the bank structures PDB50 or PDB70, they are updated periodically, and correspond to the list of structures present in the PDB clusters50.txt and clusters70.txt files delivered with the PDB standard distribution. You can have an "html'ized" look at these banks in clicking the following links where the PDB identifiers of the PDB50 or PDB70 are listed, together with their equivalent proteins (i.e. structures which have been evinced from the PDB50-70 because of the sequence similarity between them and the cluster representative).
- For the motif sites of Catalytic Site Atlas (CSA), you can find
and download them on the CSA home page. In the 3DMSS-Sites version,
we only consider validated sites, and discard mono-residue sites.
For the individual example sites (HIV site, Serine protease, ZN site,
Calcium site), they are described and listed on the 3DMSS-SitesHelp page.
References
[1] Escan: Escalier, V., J. Pothier, H. Soldano and A. Viari "Pairwise and multiple identification of three-dimensional common substructures in proteins." J. Computational Biology (1998) 5(1):41-56.
[2] CSR: M. Petitjean "Interactive Maximal Common 3D Substructure Searching with the Combined SDM/RMS Algorithm" Comput. Chem. (1998) 22[6],463-465).