# US 7,412,332 B1 · Method for analyzing polysaccharides > Agents: this data is available as JSON from the patentgrep API and MCP server — see https://patentgrep.com/llms.txt - Number: US 7,412,332 B1 - Document ID: US7412332B1 - Status: Granted - Kind: B1 - Application number: 09/557,997 - Filed: 2000-04-24 - Granted: 2008-08-12 - Earliest claimed: 1999-04-23 - Assignees: Massachusetts Institute of Technology - Inventors: Ganesh Venkataraman; Zachary Shriver; Rahul Raman; Ram Sasisekharan; Nishla Keiser - Web page: https://patentgrep.com/patent/US7412332B1 ## CPC - C07K 1/00: General methods for the preparation of peptides {, i.e. processes for the organic chemical preparation of peptides or proteins of any length} - G16B 50/30: Data warehousing; Computing architectures - G16B 50/40: Encryption of genetic data - G16C 20/20: Identification of molecular entities, parts thereof or of chemical compositions - G16B 50/00: ICT programming tools or database systems specially adapted for bioinformatics - Y10S 707/99936: Pattern matching access - Y10S 707/99943: Generating database or data structure, e.g. via user interface - C07K: PEPTIDES (peptides in foodstuffs A23; obtaining protein compositions for foodstuffs, working-up proteins for foodstuffs A23J; preparations for medicinal purposes A61K; peptides containing beta-lactam rings C07D; cyclic dipeptides not having in their molecule any other peptide link than those which form their ring, e.g. piperazine-2,5-diones, C07D; ergot alkaloids of the cyclic peptide type C07D519/02; macromolecular compounds having statistically distributed amino acid units in their molecules, i.e. when the preparation does not provide for a specific; but for a random sequence of the amino acid units, homopolyamides and block copolyamides derived from amino acids C08G69/00; macromolecular products derived from proteins C08H1/00; preparation of glue or gelatine C09H; single cell proteins, enzymes C12N; genetic engineering processes for obtaining peptides C12N15/00; compositions for measuring or testing processes involving enzymes C12Q; investigation or analysis of biological material G01N33/00) - G16B: BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY - G16C: COMPUTATIONAL CHEMISTRY; CHEMOINFORMATICS; COMPUTATIONAL MATERIALS SCIENCE - Y10S: TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS ## Abstract A data structure, tangibly embodied in a computer-readable medium, representing a polymer of chemical units is disclosed. The data structure includes an identifier including a plurality of fields for storing values corresponding to properties of the polymer. The polymer may, for example, be a polysaccharide and the chemical units may be saccharides. Also disclosed is a computer-implemented method for determining whether properties of a query sequence of chemical units match properties of a polymer of chemical units. The query sequence is represented by a first data structure, and the polymer is represented by a second data structure, each are tangibly embodied in a computer-readable medium, including an identifier including a plurality of bit fields for storing values corresponding to properties of the query sequence and polymer, respectively. The invention also involves a notational system referred to as Property Encoded Nomenclature. ## Claims ### Claim 1 A method for determining whether monosaccharides or disaccharides of a query sequence match monosaccharides or disaccharides of a polysaccharide, wherein the query sequence is represented by a first data structure, tangibly embodied in a computer-readable medium, including an identifier that includes fields, each field for storing a value for the monosaccharides or disaccharides of the query sequence, and wherein the polysaccharide is represented by a second data structure, tangibly embodied in a computer-readable medium, including an identifier that includes fields, each field for storing a value for the monosaccharides or disaccharides of the polysaccharide, wherein one or more of the values of the second data structure correspond to the nature and degree of sulfation or acetylation of the monosaccharides or disaccharides of the polysaccharide that alone do not provide the identity of the monosaccharides or disaccharides, the method comprising acts of: (A) a user providing input for the fields of the first data structure with an input device, wherein one or more of the values of the first data structure correspond to the nature and degree of sulfation or acetylation of the monosaccharides or disaccharides of the query sequence that alone do not provide the identity of the monosaccharides or disaccharides; (B) generating masks with the values stored in the fields of the first data structure; (C) performing binary operations on the values stored in the fields of the second data structure with the masks to generate results; and (D) determining whether the monosaccharides or disaccharides of the query sequence match the monosaccharides or disaccharides of the polysaccharide with the results; wherein the polysaccharide comprises disaccharide repeat units comprising hexosamine and glucuronic or iduronic acid that are linked by α/β1→4 glycosidic linkages. ### Claim 2 (depends on 1) The method of claim 1, wherein each of the fields of the first and second data structures is a bit field. ### Claim 3 (depends on 1) The method of claim 1, wherein each of the fields of the first and second data structures is a non-character based field. ### Claim 4 (depends on 1) The method of claim 1, wherein each of the identifiers of the first and second data structures is represented as a numerical identifier. ### Claim 5 (depends on 4) The method of claim 4, wherein each of the identifiers of the first and second data structures is represented as a single digit hexadecimal number. ### Claim 6 (depends on 4) The method of claim 4, wherein each of the identifiers of the first and second data structures is represented as a decimal value. ### Claim 7 (depends on 6) The method of claim 6, wherein the decimal value can be reduced to a plurality of prime divisors. ### Claim 8 (depends on 1) The method of claim 1, wherein the monosaccharides or disaccharides of the polysaccharide are monosaccharides. ### Claim 9 (depends on 1) The method of claim 1, wherein the monosaccharides or disaccharides of the polysaccharide are disaccharides. ### Claim 10 (depends on 1) The method of claim 1, wherein the values corresponding to the monosaccharides or disaccharides of the polysaccharide correspond to one or more properties of the monosaccharides or disaccharides of the polysaccharide. ### Claim 11 (depends on 10) The method of claim 10, wherein the one or more properties comprise the identity of the monosaccharides or disaccharides of the polysaccharide. ### Claim 12 (depends on 10) The method of claim 10, wherein the one or more properties comprise the exact chemical structure as defined by the basic building block of the polysaccharide. ### Claim 13 (depends on 10) The method of claim 10, wherein the one or more properties comprise the charge of the monosaccharides or disaccharides of the polysaccharide. ### Claim 14 (depends on 10) The method of claim 10, wherein the one or more properties comprise the molecular weight of the monosaccharides or disaccharides of the polysaccharide. ### Claim 15 (depends on 10) The method of claim 10, wherein the one or more properties comprise the nature and degree of sulfation of the monosaccharides or disaccharides of the polysaccharide. ### Claim 16 (depends on 10) The method of claim 10, wherein the one or more properties comprise the nature and degree of acetylation of the monosaccharides or disaccharides of the polysaccharide. ### Claim 17 (depends on 10) The method of claim 10, wherein the one or more properties comprise the nature or identity of substituents of the monosaccharides or disaccharides of the polysaccharide. ### Claim 18 (depends on 10) The method of claim 10, wherein the act of determining includes an act of determining that one or more properties of the monosaccharides or disaccharides of the query sequence match the one or more properties of the monosaccharides or disaccharides of the polysaccharide when the at least one result has a non-zero value. ### Claim 19 (depends on 1) The method of claim 1, wherein the at least one binary operation includes at least one logical AND operation. ### Claim 20 (depends on 2) The method of claim 2, wherein the at least one binary operation includes acts of performing a logical AND operation on the values stored in the bit fields of the second data structure using each of the masks to generate intermediate results, and combining the intermediate results using at least one logical OR operation to generate the results. ### Claim 21 A method for determining whether a disaccharide of a query sequence matches a disaccharide of a polysaccharide, wherein the query sequence is represented by a first data structure, tangibly embodied in a computer-readable medium, including an identifier that includes one or more fields, each field for storing a value for the query sequence, and wherein the polysaccharide is represented by a second data structure, tangibly embodied in a computer-readable medium, including an identifier that includes one or more fields, each field for storing a value for the polysaccharide, wherein the second data structure comprises one or more values that indicate whether the polysaccharide contains an iduronic or glucuronic acid, the method comprising acts of: (A) a user providing input for the one or more fields of the first data structure with an input device; (B) generating at least one mask with the value or values stored in the one or more fields of the first data structure; (C) performing at least one binary operation on the value or values stored in the one or more fields of the second data structure using the at least one mask to generate at least one result; and (D) determining whether the disaccharide of the query sequence match the disaccharide of the polysaccharide with the at least one result; wherein the polysaccharide comprises disaccharide repeat units comprising hexosamine and glucuronic or iduronic acid that are linked by α/β1→4 glycosidic linkages. ### Claim 22 (depends on 10) The method of claim 10, wherein the one or more properties comprise the presence or absence of iduronic or glucuronic acid. ### Claim 23 (depends on 21) The method of claim 21, wherein one or more of the values of the second data structure correspond to the nature and degree of sulfation or acetylation of the disaccharide of the polysaccharide.