Apparatus and method for searching protein active site
AssigneeElectronics and Telecommunications Research Institute
InventorsDae Hee Kim, Sung Hee Park, Chan Yong Park, Seon Hee Park
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Abstract
Provided are an apparatus and method of searching a protein active site. The apparatus includes a database which stores information on a plurality of reference active sites, a comparing unit which calculates 3D structural similarities according to the number of overlapping residues, with respect to an input active site and the stored reference active site, and a search unit which searches the reference active site with respect to the input active site according to the similarities. Accordingly, similar active sites can be searched with a low computational complexity, thereby be used for a correct new drug design.
Claims10
An apparatus for searching a protein active site, the apparatus comprising:
- a database which stores information on a plurality of reference active sites, wherein the information comprises coordinate data of N, Cα, and C atoms of a residue included in the reference active site, and an orthonormal vector set of the residue included in the reference active site;
- a location matching unit which matches locations of all residues included in an input active site and all residues included in the reference active site, so that at least one of the residues included in the input active site and at least one of the residues in the reference active site overlap,
- wherein the location matching unit comprises:
- a vector calculating unit which calculates an orthonormal vector set of each residue included in an input active site based on the coordinate data of the N, Cα, and C atoms of the residue in the input active site;
- and
- a converting unit which performs a rotation transform and a shift transform with respect to the coordinate data of N, Cα, and C atoms of the residue included in the input active site and the coordinate data of the N, Cα, and C atoms of the residue included in each of the reference active sites, by using the calculated orthonormal vector set and a stored orthonormal vector set;
- a similarity calculating unit which determines that a residue overlaps when transformed coordinate data of the N, Cα, and C atoms of the residue included in the input active site and the transformed coordinate data of the N, Cα, and C atoms of the residue included in the reference active site match and calculates 3D structural similarities based on the number of residues overlapping between the input active site and the reference active site;
- a search unit which searches the reference active sites while referring to the input active site according to the calculated 3D structural similarities;
- and
- a display unit which displays the searched reference active sites.
A method of searching a protein active site, the method being implemented by a machine readable program code which is embodied on a computer readable medium and configured for execution by a computer, the method comprising:
- storing information on a plurality of reference active sites in a database accessible by the computer, wherein the information comprises coordinate data of N, Cα, and C atoms of a residue included in the reference active site, and an orthonormal vector set of the residue included in the reference active site;
- matching locations of all residues included in an input active site and all residues included in the reference active site, so that at least one of the residues included in the input active site and at least one of the residues in the reference active site overlap,
- wherein the matching of locations comprises:
- calculating an orthonormal vector set of each residue included in an input active site based on coordinate data of the N, Cα, and C atoms of the residue in the input active site;
- and
- performing a rotation transform and a shift transform with respect to the coordinate data of N, Cα, and C atoms of the residue included in the input active site and the coordinate data of the N, Cα, and C atoms of the residue included in each of the reference active sites, by using the calculated orthonormal vector set and a stored orthonormal vector set;
- determining that a residue overlaps when the transformed coordinate data of the N, Cα, and C atoms of the residue included in the input active site and transformed coordinate data of the N, Cα, and C atoms of the residue included in the reference active site match;
- calculating 3D structural similarities based on the number of residues overlapping between the input active site and the reference active site;
- searching the reference active sites while referring to the input active site according to the calculated 3D structural similarities;
- and
- converting the searched reference active sites into a signal for displaying the searched reference active sites using a display operatively associated with the computer.
Dependencies are inferred from the claim text.