Methods and Systems for Identification of a Protein Binding Site
AssigneeLaboratory Corporation of America Holdings
InventorsMark Evans, Mojgan Haddad
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Abstract
Processes for identification of binding sites on protein molecules such as epitopes are provided. The disclosed methods in some embodiments use a combination of protein sequence data, structural information, experimental data on binding affinity, and computational modeling in order to identify binding sites on protein molecules. Systems and computer readable media for implementing the disclosed methods are provided. Also provided are compositions comprising a binding site or antibody that interacts with the binding site as an active ingredient and methods of using such compositions.
Claims20
A method for identifying a ligand binding site of a protein, comprising:
- a. obtaining sequence information for a plurality of sequence variants of the protein;
- b. obtaining affinity data or a viable surrogate of affinity data of each of the plurality of the sequence variants for the ligand;
- c. using a three-dimensional model of the protein's structure to define areas on the protein structure containing a plurality of residues within close proximity of each other;
- d. correlating the sequence variability within each of the areas with the affinity data for each sequence variant, wherein the information on the sequence variability within each area and the affinity data for each sequence variant is represented in a non-binary or binary form, compiled as a vector file, and processed by two or more computational methods testing each area for an ability of the sequence variability within the area to predict changes in the affinity;
- and
- e. identifying the residues forming the binding site by comparing the results obtained with the two or more computational methods.
A system for identifying a ligand binding site of a protein, comprising:
- a computer readable medium;
- and
- a processor in communication with the computer readable medium, the program configured to:
- receive sequence information for a plurality of sequence variants of the protein;
- receive affinity data or a viable surrogate of affinity data of each of the plurality of the sequence variants for the ligand;
- receive data regarding a three-dimensional model of the protein's structure;
- apply two or more computational methods to the data;
- compare the results obtained by applying the computational methods;
- and
- identify at least one residue forming the binding site.
Dependencies are inferred from the claim text.