Software for Quantifying Ligand Binding Site Burial in Proteins

Background: While defining the linear sequence of proteins is trivial, the conversion of the 2-dimentional sequence into useful, 3-dimentional information has proven to be extraordinarily difficult. Most current methods are extremely labor-intensive and yield only qualitative or relative measurement of features (e.g., ligand binding site burial).

Technology Description: A method for partitioning a protein into sectors is used to locate surface crevices and the hydrophobic core of the protein. Two complementary algorithms are configured as software, which is used to provide a quantitative measure of the degree of burial of a ligand-binding site (LBS) in a protein.

Advantages: The application of quantitative, validated methods may:

  • Improve the ability to intelligently design drugs and novel proteins dedicated to a specific purpose.
  • Streamline the process of selecting a lead candidate or a given purpose.
  • Simplify the study of binding sites.
  • Provide important information about protein dynamics.

State of Development: The working prototype has been validated by comparing findings to known features defined for 67 published proteins (see Laskowski et. al).

Related Materials:

Keywords: active site, algorithm, drug design, tertiary, protein, structure, core, crevice, enzyme, conformation, binning, hydrophobic, hydrophobicity, rational design, rational drug design

Case Numbers: SD2008-086 and SD2008-087

Inquiries To: invent@ucsd.edu