Soluble HLA ligand database utilizing predictive algorithms and methods of making and using same

• US 20020156773A1
• Filed: 02/21/2002
• Published: 10/24/2002
• Est. Priority Date: 02/21/2001
• Status: Abandoned Application

• Current Assignee: University Of Oklahoma Health Sciences Center (University of Oklahoma)
• Original Assignee: University Of Oklahoma Health Sciences Center (University of Oklahoma)
• Inventors: Prilliman, Kiley R., Hildebrand, William, Hickman, Heather D.
• Application Number:
  US10/082,034
• Publication Number:
  US 20020156773A1
• Time in Patent Office: Days
• US Class Current: 707/3
• CPC Class Codes: A61K 2039/55555 Liposomes; Vesicles, e.g. nanoparticles; Spheres, e.g. nanospheres; Polymers
• CPC Class Codes: A61K 2039/605 MHC molecules or ligands thereof
• CPC Class Codes: A61K 2039/622 non-covalent binding
• CPC Class Codes: A61K 39/385 Haptens or antigens, bound to carriers
• CPC Class Codes: A61K 39/39 characterised by the immunostimulating additives, e.g. chemical adjuvants
• CPC Class Codes: A61K 9/1272 with substantial amounts of non-phosphatidyl, i.e. non-acylglycerophosphate, surfactants as bilayer-forming substances, e.g. cationic lipids with cholesterol as the only non-phosphatidyl surfactant A61K9/127; lipids as modifying agent A61K47/543
• CPC Class Codes: C07K 14/005 from viruses
• CPC Class Codes: C07K 14/47 from mammals
• CPC Class Codes: C07K 14/4702 Regulators; Modulating activity
• CPC Class Codes: C07K 14/4728 Calcium binding proteins, e.g. calmodulin
• CPC Class Codes: C07K 14/70539 MHC-molecules, e.g. HLA-molecules
• CPC Class Codes: C07K 14/70571 for neuromediators, e.g. serotonin receptor, dopamine receptor
• CPC Class Codes: C07K 14/78 Connective tissue peptides, e.g. collagen, elastin, laminin, fibronectin, vitronectin or cold insoluble globulin [CIG]
• CPC Class Codes: C07K 2319/00 Fusion polypeptide
• CPC Class Codes: C12N 2740/16122 New viral proteins or individual genes, new structural or functional aspects of known viral proteins or genes
• CPC Class Codes: C12N 9/1247 DNA-directed RNA polymerase (2.7.7.6)
• CPC Class Codes: C12N 9/6421 from mammals
• CPC Class Codes: G01N 33/5008 for testing or evaluating the effect of chemical or biological compounds, e.g. drugs, cosmetics
• CPC Class Codes: G01N 33/5091 for testing the pathological state of an organism

Abstract

The present invention generally relates to a MHC ligand database populated with MHC ligand sequences, motifs, extended motifs, submotifs, ligands unique to infected cells, tumor specific ligands, as well as a collection of current and future developed MHC ligand sequences developed by alternative methods. Other than the ligand sequences developed by alternative methods (which are in many cases non-standardized), the remaining ligand sequences are obtained in a standardized and minimum-variable dependent manner from soluble HLA molecules constructed according to the methodology described herein. The present invention further includes methodologies incorporating linear and predictive algorithm searching and comparison utilities.

Claims

1. A method of accessing soluble HLA ligand data stored in a database comprising the steps of:

providing a database containing soluble HLA ligand data stored therein;

providing a means for accessing the database via a remote connection; and

providing a means for searching the soluble HLA ligand data stored in the database via the remote connection.

2. A computer system for a soluble HLA ligand database, comprising:

a soluble HLA ligand database stored on memory media associated with the computer system, the soluble HLA ligand database having soluble HLA ligand data stored therein; and

a data retrieval process that includes instructions for;

receiving a request from a request for general soluble HLA ligand data and returning the retrieved data to the request,

receiving a match request from the request for soluble HLA ligand data and returning data that matches the match request to the request, and p2 receiving a predictive request from the requestor for soluble HLA ligand data and returning data that matches the predictive request to the requester.

3. A soluble HLA ligand database assembled according to the methodology comprising the steps of:

providing a computer system capable of storing soluble HLA ligand data as a database on a memory media;

producing soluble HLA having ligands loaded thereon;

isolating the loaded ligands from the soluble HLA;

sequencing the loaded ligands to obtain soluble HLA ligand data; and

populating the database with the soluble HLA ligand data.

4. The soluble HLA ligand database of claim 3, further comprising the step of linearly manipulating the soluble HLA ligand data in the database.

5. The soluble HLA ligand database of claim 3, further comprising the step of manipulating the soluble HLA ligand data in the database with a predictive algorithm.